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Old 12-15-2016, 03:22 AM   #1
SS00
PhD Student
 
Location: La Jolla

Join Date: Jun 2012
Posts: 33
Question RNA-seq: Population diversity for a gene based on normalized counts?

Hi all,

A little Bioinformatics/Population Genetics question. I have a list of significant differentially expressed genes from two experimental conditions (each with 5 biological replicates). I have compared this to DE genes reported in previous literature (about 6 studies) to see how consistent these are, which I have done nicely using upSetR.

What I want to do now is to see if consistency in literature correlates with consistency in the experimental group, e.g. if a gene is upregulated in all biological replicates in condition 2, is it more likely to be reported in the majority of the other studies as opposed to a gene which is upregulated in only 3 out of the 5 replicates. To do this, I thought of converting my normalized counts for each DE gene (about 150 genes) into some sort of diversity index and visualizing this against literature consistency.

Does anyone know how to do this? In my undergrad studies I briefly dabbled in population genetics in regards to repeat polymorphisms using Fixation Index and diversity index but I am not sure how to apply this to normalized counts (e.g. 600cpm, 200cpm) instead of genotype (e.g. AA, AT).

Any thoughts appreciated. Thanks!
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