Working with 6 libraries and David

Today we extended the skills we learned working with the full transcriptome to a file of the contig counts for the six sea stars.

Here’s my notebook, which I think will update when the mirror is refreshed –

In short, this recounts our work in the morning looking at the counts file and conducting analysis for significantly differentially expressed genes using an awesome new R package – DESeq2. In the afternoon, I joined the DESeq results of differentially expressed genes to their Swiss Prot IDs and input this information into DAVID to begin looking at enrichment. We were all fascinated to see the enrichment of many immune-related processes!

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Still, the homology is a key consideration as highlighted in my list of 10 genes below.

We  worked with the transcriptome to explore which genes are included. I made a different graph of the data (an alternative to yesterday’s pie chart) in Google Fusion of the various categories:

This should be a public link.

Here are 10 genes I thought were interesting in the total transcriptome:

1. This is from a finch = Geospiza fortis immunoglobulin mu binding protein 2 (IGHMBP2), mRNA

2. But at least this immune gene is from a sea urchin = Strongylocentrotus purpuratus immunoglobulin-binding protein 1-like (LOC580592), mRNA

3. And another – Strongylocentrotus purpuratus LIM and senescent cell antigen-like-containing domain protein 2-like (LOC588224), mRNA

4. And an urchin apoptosis regulator (!) – Strongylocentrotus purpuratus apoptosis regulator BAX-like (LOC586236), mRNA

5. This is a rodent immune gene – Spermophilus tridecemlineatus progesterone immunomodulatory binding factor 1 (Pibf1), mRNA

What are these adaptive immunity homologs doing?

6. A stress-related gene from bees – Apis florea stress-activated protein kinase JNK-like (LOC100872795), mRNA

7. An interesting one from Firmicutes bacteria – Staphylococcus aureus antibiotic resistance island carrying fusB: SaRIfusB, strain CS6-EEFIC

8.  A complete viral genome – Propionibacterium phage P105, complete genome

9. A bony fish apoptosis inhibitor – Salmo salar apoptosis inhibitor 5 (api5), mRNA

10. Frog apoptosis inhibitor – Xenopus tropicalis apoptosis antagonizing transcription factor, mRNA (cDNA clone MGC:197699 IMAGE:9040231), complete cds



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