DM Notes 2.04.16

Questions to work on in our groups of three (capture electronically when applicable):

What do we want out of our research? What's the perfect outcome? How do we get there?

Goal: find all of the differentially expressed genes between samples. Perfect outcome is having a few genes that look like they're setting this digestive process in motion. What is this gene encoding for? Why is this the trigger?

What do we need to do with each of our twelve data sets, to evaluate it/know how to treat it downstream?

So far, we've looked at liver vs intestine, fed vs not fed. Dustin is going to compare all fed versus all non fed organs to get common expression across all organs. What exactly is this heat map representing? Go into DESeq documentation and read up on exactly how it calculated log change. Some things to do: get the list of genes from the heat map, bin those genes by function. For six intestine samples, verify that we have the tissue we need (hopefully mucosa, proximal, but we might have serosa, distal, etc.) Find genes specific to mucosa, other portions, look at that in each of the 6 samples. Another question: how do we account for genetic differences between snakes?

Perhaps write our own script normalizing read numbers, then comparing across samples.

Exploring correlation: correl_explore.pdf, correl_explore_scenarios.xls