New DEG list comparing temperature - annotation, enrichment; annotation of oyster differentially abundant protein list

Today I worked with the new DEG list from DESeq2 - comparing elevated (10˚C) and decreased (4˚C) temperature treatments. Annotated with uniprot-SP-GO and used DAVID to get enriched biological processes. Additionally, since it could be interesting to compare between oyster and crab projects, I annotated the list of differentially abundant proteins from the oyster project.

NEW DEG list

Analysis in DESeq2 performed by SR. Then I went through script.

Comparison –> libraries 8+10 to libraries 9+11 (new crab paper table 1)
USED SAME TRANSCRIPTOME AS THE ONE USED FOR THE INFECTED STATUS DEG COMPARISON (transcriptome v. 1.5)

In new repo for paper: RobertsLab/paper-crab

Rmd for DESeq2 –> scripts/02-DeSeq-Temperature.Rmd

List of 423 differentially expressed genes: analyses/DEG-temperature.tab

Annotation

I did the same process that I did for the previous DEG list comparing infection statuses. However the .tab DEGlist output from DESeq2 has the Trinity IDs as row names, not as a column, so in order to name the Trinity IDs column as “Trinity_ID” for join-ing purposes, I opend file up in excel and named the first column (analyses/DEG-temperature.txt).

  1. Annotated the 423 DEG list with uniprot-SP-GO.sorted and blast output from the transcriptome (v. 1.5): scripts/annotate-temp-DEGlist.Rmd
  2. Resulting file: analyses/pool_temp-annot_DEGlist.tab

The same thing happened here as with the infection status annotation –> the annotated list has more rows that the original list of 423 DEGs… likely because the transcriptome blast output has duplicate Trinity IDs listed. Therefore, the number of annotated DEGs (339) is likely not a true number. Still need to figure out how to fix this.

(also need to fix that in the infections status DEG list annotation: RobertsLab/project-crab/blob/master/scripts/annotate-2019infection_status-DEGs.Rmd)

Oyster: annotated list of differentially abundant proteins

I had a list of differentially abundant proteins already, but it wasn’t annotated with GO or the C. gigas blat output. So I did that:
R script: scripts/03-join-annotate-diffexp-prot.R
Annotated list: analyses/diff_abundant-prot-annotated.tab

There were 69 differentially abundant proteins. The number was gotten by using a cut-off of >2 log2 fold change and <-2 log2 fold change from the list of 2,808 detected proteins in the samples.

Next steps for thesis work:

this week:

  • analyses for more crab results - differential expression analsyes for temperature, probably some heat maps, look at variation of certain DEGs across all libraries, …
  • practice talk Friday: working on flow of information - will be a very rough run-through. Defense date June 2nd.

Before defense:

  • maybe do some comparisons between oyster and crab differentially abundant/expressed lists…?

before turn in thesis (due by June 26th at latest):

  • write introduction to thesis tying two projects together (maybe also a conclusion tying the results together?)
Written on May 18, 2020