February 16, 2016

Classwork

• Still trying to do searches by gene ontology terms
• Still trying to figure out if our organ samples are good samples (using DEseq?)
  • DEseq = differential expression of RNA-seq
  • Which ones should we continue on with

David wasn't great and only works for humans and needs gene I.D.'s for Python genes which don't exist

DEseq notes- reports the number of reads assigned to each gene

"To contrast two conditions, e.g., to see whether there is di�erential expression between conditions\untreated"and\treated", we simply call the function nbinomTest . It performs the tests as described in [1] and returns a data frame with the p values and other useful information" Need to test things in replicate when dealing with a biological experiment. Personally, I do not have the programming or genomics background to make sense of the DEseq link provided in the syllabus.

LOOK FOR HOUSE KEEPING GENE:

• Started by looking in Intestine Result folder in BIO343 folder.

Intestine 4 fed:

• searched transcription factor, then googled each one to find out what they do
  • transcription factor_2 Gallus Gallus
    • COUP transcription factor 2
      • necessary for expression of chicken ovalbumin gene
      • biological process is negative regulation of endopeptidase activity

Intestine Blast interesting genes highlighted in red- looking at these to figure out if we can use them/ if they are only in the intestine/ if they can help us verify our tissue sample. For Thursday, share what we've found (I don't think I've found anything), BUT we are trying to verify all 12 samples to make sure which ones we should carry on with. Dr. Campbell and Dr. Heyer compared liver fed to no_fed and found 3 transcription factors, then they want to change the way it clusters and look at all the genes that correlate with those transcription factors (supervised cluster).

• • • "species = human"

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