Difference between revisions of "Emilie Uffman"
| Line 8: | Line 8: | ||
| + | ---- | ||
| + | |||
Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon): | Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon): | ||
| Line 23: | Line 25: | ||
**See Jon's notes for information on question** | **See Jon's notes for information on question** | ||
| + | |||
| + | |||
| + | ---- | ||
Filtered data on galaxy to remove data with 'NA' | Filtered data on galaxy to remove data with 'NA' | ||
| Line 54: | Line 59: | ||
https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=1058 | https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=1058 | ||
| + | |||
| + | |||
| + | CENP-A expression decreases in senescent cells | ||
| + | |||
| + | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/ | ||
| + | |||
| + | At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule | ||
| + | |||
| + | https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso | ||
| + | |||
| + | -Black Lab discoveries give insight into genetic inheritance | ||
| + | -CENP-A could be the 'key' epigenetic marker protein | ||
| + | -CENP-A changes shape of the nucleosome | ||
| + | |||
| + | ---- | ||
'''Excel tools:''' | '''Excel tools:''' | ||
Truncate numbers in excel: =left (A1, 18) | Truncate numbers in excel: =left (A1, 18) | ||
Revision as of 22:42, 7 February 2017
Comparison of maternal trisomy and disomy (CB131,126,117,125,122,121) with Paternal trisomy and disomy (CB091,089,087,093,100,103)
-the limited variation in paternal disomy and trisomy is conserved
-maternal still has variation
-there is no clear divide between gender along PC1--what does this mean?
Sorting of paternal trisomy data(Emilie) and maternal trisomy data (Jon):
Use galaxy sort tool to sort p-value in ascending order
Why is it that for many of the data there is a base mean and all statistics but no p-value?
ENSMUST00000000674.12 Base mean: 8.06384358972545 LogFC: 0.0460016853044759 Std Error: 0.0883691926491015 Wald-Stats: 0.520562471212569 P-value: NA P-adjusted: N
- See Jon's notes for information on question**
Filtered data on galaxy to remove data with 'NA' -skip 0 header line- Only retained 70.41% of data when filtering to remove 'NA'
Copied data to excel and use shortcut to removal decimals without rounding
Copy (100lines of) data into MGI Database
http://www.informatics.jax.org/batch/summary#myDataTable=results%3D25%26startIndex%3D0
CENPA Gene (Centromere Protein A) located on Chromosome 5, 16.76
"Phenotype Overview: cardiovascular system, cellular, craniofacial, embryo, growth/size/body, mortality/aging, nervous system"
"A mutation in this gene can cause chromosomal missegregation, aneuploidy and apoptosis"
CENPA segmental haploidy of chr5 in mice is known to cause Wolf-Hirschhorn syndrome -conserved synteny to human 4p16.3
Symptoms:
-'Greek warrior helmut facial appearance'
-mental retardation
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
https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=1058
CENP-A expression decreases in senescent cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615257/
At the Crossroads of Chromosomes: Penn Study Reveals Structure of Cell Division's Key Molecule
https://www.pennmedicine.org/news/news-releases/2010/september/at-the-crossroads-of-chromoso
-Black Lab discoveries give insight into genetic inheritance -CENP-A could be the 'key' epigenetic marker protein -CENP-A changes shape of the nucleosome
Excel tools: Truncate numbers in excel: =left (A1, 18)
