2/04/16

Notes 2/04/16

What do we want out of our research? What is the perfect outcome?

We want to find the genes that are differentially expressed between unfed and fed snakes and figure out their role in organ growth. The perfect outcome would be to find the gene that starts the cascade.

How do we get there?

First, we need to actually look at the snakes to decide if it’s reasonable to group fed and unfed because form preliminary data that may not make sense. If we can’t group in this manner, we need to find a new way or grouping similar data. We need to figure out how to run a program to see a list of the genes that are differentially expressed. We also need to figure out a way to prioritize (threshold) the differentially expressed genes that will focus further on. From here, we need to research these genes further to attempt to place them within their physiological function or pathway.

What are we going to do with each of our 12 data sets? To evaluate it in order to know how to treat it downstream

First, we only care about our six intestine data sets. Focusing in on our intestine genes, we’d first like to try to find a gene unique to the intestine in order to verify our tissue sample. Using our data that includes each snake, gene, and number of normalized transcripts we would do the following: • Average (maybe, have to look at grouping) across unfed and fed expression, compare those averages and set a percent difference to determine significant differential gene expression • A good picture for our presentation would be a heat map of just these genes • What to do with protein of unknown function?? Maybe first run through discard and see if we can get significant results with known genes • Grouping: hopefully we may be able to discount something based on findings from our intestine housekeeping gene investigation

Notes from discussion: How will we define a biological function that fits the definition of starting the cascade? Genes involved in amino acid uptake, could be transporter, (this isn’t really what we think of when thinking of cascades) maybe a g-protein that later on activates growth protein (we should potentially see transcript production here unless its already there) !A transcription factor (a transcript for a transcription factor would be ideal)! Go back and try to find source of proteins!! Cell division or loosely fitting in category of hypertrophy would also be an ok thing to look for

Under-expression might be relevant (we should cover this if we have a percent difference threshold)

Serosa v. mucosa, find housekeeping gene specific not only to small intestine but to a particular layer of the small intestine (sugar/amino acid uptake should be found in mucosa)

Potentially use dendograms to figure out threshold on heatmaps we’ve done so far

Separate out statistically what is interesting v. biologically

Second route: pull out all genes that are transcription factors then see if there is any difference between fed and unfed within this smaller grouping