Feb 04

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

Gene cascade initiation. what is causing the liver to grow? What starts everything?

Hypertrophy vs replication, is the same in Liver as it is in intestines? Hyperplasia vs apoptosis?

Cell signaling, G proteins that come after a ligand binding to a receptor. The ligand/receptor could already be present so we wouldn't see that. Towards the bottom of the cascade we could find the protein that causes the enlargement of Liver.

We want to see a transcription activator.

We have to look at transcripts because we aren't looking at proteins. (Source of these proteins: ......)

Steps:

Look for extreme variation in expression of genes differentially expressed between fed vs non-fed.

Look at 6 our data as well to see if gene(s?) responsible for cascade is turned on/off.

Isolate genes of interest

Look for orthologs with hypertrophy, compare to python genome

Look for all of the transcription factors

2. What are we going to do with each of our 12 data sets? What do we need to do with each individual data set to know how to treat it?

See if samples were taken as expected. Look at housekeeping genes. Make sure liver is producing liver transcripts. Do a quality control on the 12 samples.

Try to find orthologs, mechanisms for enlarged organs in other organisms

Compare 3 fed vs 3 non-fed. Look at heat map

Maybe calculate STDEV and the ones with the lowest across a condition could be the most useful for comparisons.