February 18, 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.
As we began 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.
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.
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.
Housekeeping genes in Pythons: NHE3 is a sodium transporter in intestinal membrane. Let's see if it matches up with one of our samples. NHE3 article
Also look for housekeeping genes given in Castoe et all (2013). We think they provide housekeeping genes
Note: Ashlyn left class early this day to travel for Track & Field competition.
