Difference between revisions of "February 18, 2016"

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(Created page with "Dr. C and Dr. Heyer made cool progress. We did not do Euclidian distance, we looked at CORRElATION, we can also do absolute value. p value = 0.01 instead of 0.05 so that we ...")
 
 
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Dr. C and Dr. Heyer made cool progress.
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== Classwork ==  
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We did not do Euclidian distance, we looked at CORRElATION, we can also do absolute value.
 
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p value = 0.01 instead of 0.05 so that we get a shorter list of genes.  Document has code on it.
 
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There is a code where you can find gene names. "write.csv(colnames(carp).... if there is a seed gene we want genes most correlated to that one. Theres a lot of really good candidate genes! 
 
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Transcription factors are not always transcribed in high quanities becuase you don't need a lot... So look for change (on vs. off) not just quantity of expression. 
 
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t in code = transforming/transposing x and y axis.  
 
  
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Tae sequences put them in Blast to Go- put in formated listed of sequences then it runs it through mapping. Sequence based method...
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Dr. Campbell and Dr. Heyer made significant progress on coding work for correlation. They changed the p-value from 0.05 to 0.01 so that R-Studio generates a shorter list of genes. (FIND DOCUMENT WITH THE CODE ON IT). Dr. Campbell and Dr. Heyer also mentioned a code that allows us to find gene names, "write.csv(colnames(carp)..." We want to use this code to find a seed gene, and then find genes most correlated to that seed gene.
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Other group taking gene names from file and pair names of genes in gene file to gene ontology terms. Name based method...  
 
  
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All 6 are good liver samples. We still need to identify/verify intestine samples 3 and 6. Look in excel sheet Kathryn shared. Blasting over represented genes gave us genes. Look at and cite Kathryn's page. Google names on list of housekeeping genes and see if we can verify/decode/match differences in names to verify tissue samples.  
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Other groups in the class are working formatting sequence lists. One group is using Blast 2Go while another group is using gene names from a file and pairing them with gene ontology terms to format sequences with a sequence-based method or name-based method, respectively.
  
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Housekeeping genes in Pythons:  NHE3 is a sodium transporter in intestinal membrane. Let's see if it matches up with one of our samples. [http://www.annualreviews.org/doi/full/10.1146/annurev.physiol.67.031103.153004  NHE3 article]
 
  
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''Coding Notes:'' 
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*"t" in code = transforming/transposing x and y axis. 
  
  
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== Gene Search == 
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All six liver samples are viable. However, we still need to verify intestine samples 3 and 6.
  
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After attaining a list of genes from a previous blast of over represent genes, we tried to match these genes with genes in intestine samples 3 and 6. We googled the names of housekeeping genes from [http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Notes_2/16/16 Kathryn's list of housekeeping genes] to see if we can decode the differences in gene identifications and match them to genes that would verify our tissue samples. We also attempted to find housekeeping genes given the list of genes in Castoe et al. (2013). As we continued our gene search, we remembered that transcription factors are not always transcribed in high quantities so we must look for change in expression (on vs. off) instead of only looking at quantity of expression. 
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=== Identified Genes: === 
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*Housekeeping genes in Python: 
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**NHE3: a sodium transporter in the intestinal membrane. 
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**Reference [http://www.annualreviews.org/doi/full/10.1146/annurev.physiol.67.031103.153004  NHE3 article] for more information.
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''Note: Ashlyn left class early this day to travel for Track & Field competition.'' 
  
  
  
 
[http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Ashlyn Ashlyn's Main Page]
 
[http://gcat.davidson.edu/mediawiki-1.19.1/index.php/Ashlyn Ashlyn's Main Page]

Latest revision as of 15:11, 9 March 2016

Classwork

Dr. Campbell and Dr. Heyer made significant progress on coding work for correlation. They changed the p-value from 0.05 to 0.01 so that R-Studio generates a shorter list of genes. (FIND DOCUMENT WITH THE CODE ON IT). Dr. Campbell and Dr. Heyer also mentioned a code that allows us to find gene names, "write.csv(colnames(carp)..." We want to use this code to find a seed gene, and then find genes most correlated to that seed gene.

Other groups in the class are working formatting sequence lists. One group is using Blast 2Go while another group is using gene names from a file and pairing them with gene ontology terms to format sequences with a sequence-based method or name-based method, respectively.


Coding Notes:

  • "t" in code = transforming/transposing x and y axis.


Gene Search

All six liver samples are viable. However, we still need to verify intestine samples 3 and 6.

After attaining a list of genes from a previous blast of over represent genes, we tried to match these genes with genes in intestine samples 3 and 6. We googled the names of housekeeping genes from Kathryn's list of housekeeping genes to see if we can decode the differences in gene identifications and match them to genes that would verify our tissue samples. We also attempted to find housekeeping genes given the list of genes in Castoe et al. (2013). As we continued our gene search, we remembered that transcription factors are not always transcribed in high quantities so we must look for change in expression (on vs. off) instead of only looking at quantity of expression.


Identified Genes:

  • Housekeeping genes in Python:
    • NHE3: a sodium transporter in the intestinal membrane.
    • Reference NHE3 article for more information.



Note: Ashlyn left class early this day to travel for Track & Field competition.


Ashlyn's Main Page

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