DML Analysis Part 7

DML-mRNA Gene Enrichment

My revised blastx finished running over the weekend! The output can be found here. I emailed the revised blast output and original transcript file to Mike Riffle in Genome Sciences so he could modify the gene enrichment tool.

DML-mRNA Gene Enrichment

In my R Markdown file, I merged the transcript-uniprot blast results with the DML-mRNA overlap file. I exported the results in this file.

I isolated the Uniprot accession codes so I could do a standard DAVID gene enrichment. I unfolded columns in both the transcript blastx results and DML-mRNA overlaps and saved them as new files. I also saved the Uniprot codes for the background (transcripts) and gene list (overlaps) in this document.








I saved the DAVID output in this folder. I downloaded information for all functional annotations, as well as individual lists for biological processes, cellular components, and molecular functions.

I wanted to use ReVIGO to visualize significant GOterms, but ReVIGO’s interactive graphic wasn’t loading after I pasted a list of GOterms and p-values! I posted this issue. I have the option to download an R script to create the graphic, which would be useful, but also extremely tedious for image formatting. If I don’t hear anything by tomorrow morning, I’ll need to download the R scripts. My goal is to present the DML-mRNA enrichment results at PCSGA.

DML-Exon Gene Enrichment

Steven confirmed I need to do a gene enrichment for DML-exon, DML-intron, flanking regions, and all regions combined. I thought I could get started on these enrichments, even though I’ll probably concentrate on the DML-mRNA enrichment for my PCSGA talk. However, the DML-exon file doesn’t have the same transcript IDs the DML-mRNA and blastx results do. The DML-exon and DML-intron files only have chromosome IDs, positions, and strand information. I posted another issue asking if it made sense to merge the DML-exon or DML-intron files with the original mRNA gff to obtain transcript IDs. If it doesn’t, I’ll need to figure out another way to do that gene enrichment.

Going forward

While I wait for the verdict on my two open issues, I’m going to start drafting my PCSGA talk, focusing on the DML-mRNA enrichment. I saw lots of significant GOterms related to reproduction and growth, so that will be interesting to explain!

Written on September 11, 2018