All that glitters is not enrichment

This afternoon we started a coordinated approach to the differentially expressed genes in the sea star transcriptome. While we have ideas lined up for additional analyses of the transcriptome that are bound to prove fruitful, we are currently concentrating efforts on understanding the genes that belong to enriched processes.

After constructing a detailed filtering process for prioritizing which genes to look at, we divided up the 3 enriched processes among the group of people working on the transcriptome. I at first thought it would be important to coordinate, but it was pointed out that we could learn a lot by the different stories and interpretations people bring to the table after analyzing the same subset of genes. I started an in-depth look at the genes involved in the “cytokines” enriched process.  The other two groups are immune function and cellular adhesion.

I’m still in the process of going through genes, but it has been a really interesting exercise. My comparative immunity cap is on! I think we will be best served by finding the most specific information available on the listed genes in closely related species. Already we are finding some of them in echinoderms and even sea stars, so that will help ground our coming interpretations.

This is our work flow for a standardized sorting methodology:

1) Find the genes in your process from a master spreadsheet

2) Ensure that, for each contig, all 3 samples in one condition have values for at least one of the conditions

3) Sort by log fold change – most positive AND most negative

4) Assess if p=0.01 is necessary to give you a manageable number to work with

5) Take SPID and put it into beta.uniprot.org/uniprot/ (+your SPID)

6) Note biological functions the gene is involved with and begin literature search; offer possible interpretation(s) of the involvement in the broader biological process (i.e. immune, cell adhesion, or cytokines)

 

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