Feb 4

Research has begun in earnest.

R analysis of the RNASeq data

Questions to answer:

1. What do we want out the research. What is the perfect outcome? How do we get there?

Looking for some sort of G protein? Bottom of the G protein cascade: making proteins, but their could be transcription because they go for so long in between uptake periods. What would trigger this cascade? A transcription activator? Is it there or are we looking for that? All proteins that appear in plasma for uptake, where do the proteins originate from (in literature)? Is lipid uptake involved in the volume growth? Typically a cascade is transcription factor that turns on a whole lot, so if we can find that, that's a good lead. Hormone repsonsive transcription factor. (Extracellular and hormone receptors (goes straight through and binds to a protein to make a transcription factor)) Kegg has an RNA splicing pathway to consult.

What if we went functional first, and used GO terms to find the transcription factors first.

2. What are we going to do with each of our 12 data sets to evaluate it and know how to treat it downstream?

Validate the samples. Use the housekeeping genes in the literature (Serosa won't have any regulation around protein uptake).

Need a quality control on all the samples, before we take off on anything else.

Heat map tells is using the genes that helps us distinguish the fed from the non fed. How are they getting on the list, because that could be vital. If something has a zero value does it get thrown out or kept?