http://gcat.davidson.edu/GcatWiki/api.php?action=feedcontributions&feedformat=atom&user=Emuffman 2026-05-19T19:30:52Z User contributions MediaWiki 1.28.2 http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18983 2017-03-30T14:46:49Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> We are going to target genes that are triplicated and differentially expressed<br /> <br /> Maternal: Atp5j, Cbr1, Dopey2, Pigp, <br /> ----<br /> Prdm15<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> <br /> Paternal: 1110004E09Rik, App, C2cd2, Chaf1b, Dyrk1a, Ltn1, Mrpl39, N6amt1, Ripk4, Runx1, Sic5a3, Urb1, Wrb<br /> <br /> <br /> <br /> Today we worked with galaxy to filter out data more<br /> 1. we compared parent dependent trisomy and parent dependent disomy<br /> 2. we filtered these 2 datasets to have a pval less than 0.01<br /> 3. We merged these datasets to find those that matched in both columns<br /> 4. Then used the 'concatenate' tool to merge all <br /> 5. looking at chr 16 (Gabpa, Chaf1b, Tiam1, Jam2, Cox17)<br /> <br /> re did these steps by limiting pval to 0.001<br /> <br /> <br /> <br /> http://software.broadinstitute.org/gsea/register.jsp<br /> <br /> <br /> <br /> Genes of interest after clarifying methods for p-val,0.5: Cacna1h, Son<br /> <br /> <br /> http://www.informatics.jax.org/reference/phenotype/marker/MGI:98353?typeFilter=Literature<br /> <br /> Genes we know to be triplicated for further investigation:<br /> Cct8, Bach1, Son, Cryzl1, Runx1, Cbr1,Dscr3, Dyrk1a,<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18980 2017-03-30T14:15:56Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> We are going to target genes that are triplicated and differentially expressed<br /> <br /> Maternal: Atp5j, Cbr1, Dopey2, Pigp, <br /> ----<br /> Prdm15<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> <br /> Paternal: 1110004E09Rik, App, C2cd2, Chaf1b, Dyrk1a, Ltn1, Mrpl39, N6amt1, Ripk4, Runx1, Sic5a3, Urb1, Wrb<br /> <br /> <br /> <br /> Today we worked with galaxy to filter out data more<br /> 1. we compared parent dependent trisomy and parent dependent disomy<br /> 2. we filtered these 2 datasets to have a pval less than 0.01<br /> 3. We merged these datasets to find those that matched in both columns<br /> 4. Then used the 'concatenate' tool to merge all <br /> 5. looking at chr 16 (Gabpa, Chaf1b, Tiam1, Jam2, Cox17)<br /> <br /> re did these steps by limiting pval to 0.001<br /> <br /> <br /> <br /> http://software.broadinstitute.org/gsea/register.jsp<br /> <br /> <br /> <br /> Genes of interest after clarifying methods for p-val,0.5: Cacna1h, Son<br /> <br /> <br /> http://www.informatics.jax.org/reference/phenotype/marker/MGI:98353?typeFilter=Literature<br /> <br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18979 2017-03-30T14:07:33Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> We are going to target genes that are triplicated and differentially expressed<br /> <br /> Maternal: Atp5j, Cbr1, Dopey2, Pigp, <br /> ----<br /> Prdm15<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> <br /> Paternal: 1110004E09Rik, App, C2cd2, Chaf1b, Dyrk1a, Ltn1, Mrpl39, N6amt1, Ripk4, Runx1, Sic5a3, Urb1, Wrb<br /> <br /> <br /> <br /> Today we worked with galaxy to filter out data more<br /> 1. we compared parent dependent trisomy and parent dependent disomy<br /> 2. we filtered these 2 datasets to have a pval less than 0.01<br /> 3. We merged these datasets to find those that matched in both columns<br /> 4. Then used the 'concatenate' tool to merge all <br /> 5. looking at chr 16 (Gabpa, Chaf1b, Tiam1, Jam2, Cox17)<br /> <br /> re did these steps by limiting pval to 0.001<br /> <br /> <br /> <br /> http://software.broadinstitute.org/gsea/register.jsp<br /> <br /> <br /> <br /> Genes of interest after clarifying methods for p-val,0.5: Cacna1h, Son<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18958 2017-03-21T14:06:30Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> We are going to target genes that are triplicated and differentially expressed<br /> <br /> Maternal: Atp5j, Cbr1, Dopey2, Pigp, Prdm15<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> <br /> Paternal: 1110004E09Rik, App, C2cd2, Chaf1b, Dyrk1a, Ltn1, Mrpl39, N6amt1, Ripk4, Runx1, Sic5a3, Urb1, Wrb<br /> <br /> <br /> <br /> Today we worked with galaxy to filter out data more<br /> 1. we compared parent dependent trisomy and parent dependent disomy<br /> 2. we filtered these 2 datasets to have a pval less than 0.01<br /> 3. We merged these datasets to find those that matched in both columns<br /> 4. Then used the 'concatenate' tool to merge all <br /> 5. looking at chr 16 (Gabpa, Chaf1b, Tiam1, Jam2, Cox17)<br /> <br /> re did these steps by limiting pval to 0.001<br /> <br /> <br /> <br /> http://software.broadinstitute.org/gsea/register.jsp<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18952 2017-03-16T14:16:44Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> We are going to target genes that are triplicated and differentially expressed<br /> <br /> Maternal: Atp5j, Cbr1, Dopey2, Pigp, Prdm15<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> <br /> Paternal: 1110004E09Rik, App, C2cd2, Chaf1b, Dyrk1a, Ltn1, Mrpl39, N6amt1, Ripk4, Runx1, Sic5a3, Urb1, Wrb<br /> <br /> <br /> <br /> Today we worked with galaxy to filter out data more<br /> 1. we compared parent dependent trisomy and parent dependent disomy<br /> 2. we filtered these 2 datasets to have a pval less than 0.01<br /> 3. We merged these datasets to find those that matched in both columns<br /> 4. Then used the 'concatenate' tool to merge all <br /> 5. looking at chr 16 (Gabpa, Chaf1b, Tiam1, Jam2, Cox17)<br /> <br /> re did these steps by limiting pval to 0.001<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18948 2017-03-14T14:54:16Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> We are going to target genes that are triplicated and differentially expressed<br /> <br /> Maternal: Atp5j, Cbr1, Dopey2, Pigp, Prdm15<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> <br /> Paternal: 1110004E09Rik, App, C2cd2, Chaf1b, Dyrk1a, Ltn1, Mrpl39, N6amt1, Ripk4, Runx1, Sic5a3, Urb1, Wrb<br /> <br /> <br /> <br /> Today we worked with galaxy to filter out data more<br /> 1. we compared parent dependent trisomy and parent dependent disomy<br /> 2. we filtered these 2 datasets to have a pval less than 0.01<br /> 3. We merged these datasets to find those that matched in both columns<br /> 4. Then used the 'concatenate' tool to merge all <br /> <br /> re did these steps by limiting pval to 0.001<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18944 2017-03-14T14:42:15Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> We are going to target genes that are triplicated and differentially expressed<br /> <br /> Maternal: Atp5j, Cbr1, Dopey2, Pigp, Prdm15<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> <br /> Paternal: 1110004E09Rik, App, C2cd2, Chaf1b, Dyrk1a, Ltn1, Mrpl39, N6amt1, Ripk4, Runx1, Sic5a3, Urb1, Wrb<br /> <br /> <br /> <br /> Today we worked with galaxy to filter out data more<br /> 1. we compared parent dependent trisomy and parent dependent disomy<br /> 2. we filtered these 2 datasets to have a pval less than 0.01<br /> 3. We merged these datasets to find those that matched in both columns<br /> 4. Then used the 'concatenate' tool to merge all <br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18897 2017-02-21T15:13:03Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> We are going to target genes that are triplicated and differentially expressed<br /> <br /> Maternal: Atp5j, Cbr1, Dopey2, Pigp, Prdm15<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> <br /> Paternal: 1110004E09Rik, App, C2cd2, Chaf1b, Dyrk1a, Ltn1, Mrpl39, N6amt1, Ripk4, Runx1, Sic5a3, Urb1, Wrb<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18896 2017-02-21T14:58:49Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> We are going to target genes that are triplicated and differentially expressed<br /> <br /> Maternal: Atp5j, Cbr1, Dopey2, Pigp, Prdm15<br /> <br /> Paternal: 1110004E09Rik, App, C2cd2, Chaf1b, Dyrk1a, Ltn1, Mrpl39, N6amt1, Ripk4, Runx1, Sic5a3, Urb1, Wrb<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18887 2017-02-20T17:43:07Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> http://www.sciencedirect.com/science/article/pii/S1097276512002286<br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18886 2017-02-20T17:38:37Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> <br /> Tiam1<br /> <br /> http://www.informatics.jax.org/batch/summary<br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18885 2017-02-20T17:20:42Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958)<br /> <br /> Hmgn1<br /> <br /> Mis18a--MIS18A is required for recruitment of CENPA to centromeres and normal chromosome segregation, however if this is differentially expressed could this have an effect on the CENPA expression?<br /> <br /> http://string-db.org/cgi/network.pl?taskId=p1PAptAgQut1<br /> <br /> <br /> Tiam1<br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18884 2017-02-20T17:04:28Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> <br /> <br /> ----<br /> Genes to investigate:<br /> <br /> ETS_2 (https://www.ncbi.nlm.nih.gov/pubmed/2149958), Hmgn1, Mis18a, Tiam1)<br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18881 2017-02-16T15:45:11Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2<br /> -Chr 17: <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, Ttc3, Dscr3, Psmg1, Zbtb21 ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18880 2017-02-16T15:40:32Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2<br /> -Chr 17: <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, Donson, RUNX1, Paxb1, ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18879 2017-02-16T15:37:32Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2<br /> -Chr 17: <br /> <br /> Several genes on Chr 16 (Gabpa, Cct8, Usp16, Sod1, 1110004E09Rik,Synj1, Gart, Son, ) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18875 2017-02-16T15:23:59Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2<br /> -Chr 17: <br /> <br /> Several genes (Brwd1, RUNX1, Gabpa, Paxb1) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18873 2017-02-16T15:21:26Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2, Eif4g1<br /> <br /> -Chr 17: <br /> <br /> Several genes (Brwd1, RUNX1, Gabpa, Paxb1) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18872 2017-02-16T15:13:28Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2, Eif4g1<br /> <br /> -Chr 17: <br /> <br /> Several genes (Brwd1, RUNX1, Gabpa) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18871 2017-02-16T15:11:40Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2, Eif4g1<br /> <br /> -Chr 17: <br /> <br /> Several genes (Brwd1, Gabpa) have different transcript numbers but are located at the same location. All however, have similar logFC.<br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18860 2017-02-14T15:45:03Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2, Eif4g1<br /> <br /> -Chr 17: <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18859 2017-02-14T15:44:02Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2, Eif4g1<br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18858 2017-02-14T15:43:30Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> -Chr 16: Paxbp1, Brwd1, Gabpa, Jam2, <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18857 2017-02-14T15:35:56Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> Orange: both maternal and paternal share this gene with sig p-value and large FC<br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18856 2017-02-14T15:30:34Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (max E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> <br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18855 2017-02-14T15:30:18Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value (min E-4) to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> <br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18854 2017-02-14T15:25:02Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> Yellow: associated with Down Syndrome (from paper)<br /> <br /> <br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18852 2017-02-14T15:15:46Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value to investigate first, then sort by logFC<br /> Key:<br /> Light blue highlighter: chr 16<br /> <br /> Light green highlight: chr 17<br /> <br /> Dark purple highlight: small p-value (most significant difference)<br /> <br /> Blue highlight: both a logFC &gt;1 and small p-val<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18851 2017-02-14T14:58:27Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with most significant p-value to investigate first, then sort by logFC<br /> <br /> <br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18850 2017-02-14T14:56:37Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with fold change &gt;1.0 to investigate first<br /> <br /> Chromosome 16<br /> -APP<br /> <br /> -Dyrk1a<br /> <br /> -Runx1<br /> <br /> -Gabpa<br /> <br /> -Jam2<br /> <br /> -Eif4g1<br /> <br /> -Usf3<br /> <br /> -Son<br /> <br /> -Brwd1<br /> <br /> Chromosome 17<br /> <br /> -Tulp4<br /> <br /> -Eml4<br /> <br /> -Adgre1<br /> <br /> -Afdn<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18849 2017-02-14T14:53:47Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with fold change &gt;1.0 to investigate first<br /> <br /> Chromosome 16<br /> -APP<br /> <br /> -Dyrk1a<br /> <br /> -Runx1<br /> <br /> -Gabpa<br /> <br /> -Jam2<br /> <br /> -Eif4g1<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18848 2017-02-14T14:50:37Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with fold change &gt;1.0 to investigate first<br /> <br /> Chromosome 16<br /> -APP<br /> -Dyrk1a<br /> -Runx1<br /> -Gabpa<br /> -Jam2<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18847 2017-02-14T14:48:40Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> Methodology:<br /> <br /> 1. Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> 2. Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> 3. Copy data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> 4. Used R Studio with R Script Jon created to merge the Galaxy data and data from MGI in order to be able to look at both logFC and gene name together<br /> <br /> 5. Selected genes with fold change &gt;1.0 to investigate first<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18837 2017-02-09T15:54:53Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> sorted data by chromosome, focussing on chr 16 and 17<br /> <br /> Plan: sort data to filter for chr 16 and 17 while conserving log fold change information so we can target specific genes to investigate<br /> <br /> ----<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18833 2017-02-08T01:16:42Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp within the DS region<br /> <br /> -involved in chromatin remodeling<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> ----<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18832 2017-02-08T01:13:06Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> -located on Chr16:95992449-96082526 bp<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> <br /> <br /> ----<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18831 2017-02-08T01:11:45Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> (ENSMUST000134372) <br /> <br /> -up regulated<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> ENSMUST000153398 (Brwd1) <br /> <br /> -down regulated <br /> <br /> -associated with Down Syndrome<br /> <br /> http://www.informatics.jax.org/reference/diseaseRelevantMarker/MGI:1890651<br /> <br /> <br /> <br /> <br /> ----<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18830 2017-02-07T23:01:36Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> Going forward:Want to investigate the CENP-A gene in maternal strains<br /> <br /> ----<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18829 2017-02-07T22:44:45Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> ----<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18828 2017-02-07T22:42:32Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> ----<br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> <br /> ----<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> <br /> <br /> CENP-A expression decreases in senescent cells<br /> <br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/<br /> <br /> At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule<br /> <br /> https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso<br /> <br /> -Black Lab discoveries give insight into genetic inheritance<br /> -CENP-A could be the 'key' epigenetic marker protein<br /> -CENP-A changes shape of the nucleosome<br /> <br /> ----<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18827 2017-02-07T21:09:28Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&amp;dopt=full_report&amp;list_uids=1058<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18826 2017-02-07T21:02:18Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved synteny to human 4p16.3<br /> <br /> Symptoms:<br /> <br /> -'Greek warrior helmut facial appearance' <br /> <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18825 2017-02-07T21:01:30Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome <br /> -conserved sentence to human 4p16.3<br /> Symptoms:<br /> -'Greek warrior helmut facial appearance' <br /> -mental retardation<br /> <br /> Naf D, Wilson LA, Bergstrom RA, Smith RS, Goodwin NC, Verkerk A, van Ommen GJ, Ackerman SL, Frankel WN, Schimenti JC, Mouse models for the Wolf-Hirschhorn deletion syndrome. Hum Mol Genet. 2001 Jan 15;10(2):91-8<br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18824 2017-02-07T20:32:59Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into [[MGI Database]]<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76<br /> <br /> &quot;Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system&quot;<br /> <br /> &quot;A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis&quot;<br /> <br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18823 2017-02-07T17:45:23Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into MGI Database<br /> <br /> http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0<br /> <br /> <br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18822 2017-02-07T17:44:40Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> -the limited variation in paternal disomy and trisomy is conserved<br /> <br /> -maternal still has variation<br /> <br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into MGI Database<br /> <br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18821 2017-02-07T17:44:25Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> -the limited variation in paternal disomy and trisomy is conserved<br /> -maternal still has variation<br /> -there is no clear divide between gender along PC1--what does this mean?<br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into MGI Database<br /> <br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18820 2017-02-07T17:27:16Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> <br /> Copied data to excel and use shortcut to removal decimals without rounding<br /> <br /> Copy (100lines of) data into MGI Database<br /> <br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18819 2017-02-07T16:10:12Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> <br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman http://gcat.davidson.edu/GcatWiki/index.php?title=Emilie_Uffman&diff=18818 2017-02-07T16:09:14Z

<p>Emuffman: </p> <hr /> <div>Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) <br /> with <br /> Paternal trisomy and disomy (CB091,089,087,093,100,103)<br /> <br /> <br /> <br /> Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):<br /> <br /> Use galaxy sort tool to sort p-value in ascending order <br /> <br /> Why is it that for many of the data there is a base mean and all statistics but no p-value? <br /> <br /> ENSMUST00000000674.12 <br /> '''Base mean''': 8.06384358972545 <br /> '''LogFC:''' 0.0460016853044759 <br /> '''Std Error:''' 0.0883691926491015 <br /> '''Wald-Stats''': 0.520562471212569 <br /> '''P-value:''' NA <br /> '''P-adjusted''': N<br /> <br /> **See Jon's notes for information on question**<br /> <br /> Filtered data on galaxy to remove data with 'NA'<br /> -skip 0 header line-<br /> <br /> Only retained 70.41% of data when filtering to remove 'NA'<br /> <br /> '''Excel tools:'''<br /> Truncate numbers in excel: =left (A1, 18)</div>

Emuffman