Yaamini’s Notebook: DML Analysis Part 9

Gene Enrichment Results from compGO

Mike fixed the gene enrichment tool, so I got to use it! Good thing, becuase ReVIGO is currently down and I cannot generate gene enrichment visualizations any other way. All of this information can be found in my R Markdown analysis notebook.

The website expects inputs in the following format: sp Q9C098 DCLK3_HUMAN

This means I don’t need to unfold the specific code from anything. The tool generates both reports and images, all of which can be found in this folder. I can also do comparisons between two different lists, which is useful. I used a p-value of 1e-2, the default, for each enrichment.

DML-mRNA overlaps

bp

cc

mf

Figures 1-3. Gene enrichment visualizations for biological processes, cellular components, and molecular functions.

Exon and intron Uniprot codes

To get Uniprot codes for DML-Exon and DML-Intron overlaps, I used intersectBed with the -wao argument to find overlaps between these two files and the mRNA gff. -wao allowed me to write out the overlaps between the DML-Exon or DML-Intron file with the mRNA and count the number of overlaps. If there was no overlap (which was unlikely), then the DML-Exon or DML-Intron file information was written out with NULL to indicate that particular exon or intron had no overlap in the mRNA file. I looked at the DML-Exon file in particular, and found it was really large. There seem to be a bunch of repeating lines. Not sure if that’s just because several genome chunks lead to different mRNAs, and thus, different exon patterns, or if there was a problem with the -wao argument. This is something I will need to clean up after PCSGA.

DML-Intron overlaps

bp

cc

mf

Figures 4-6. Gene enrichment visualizations for biological processes, cellular components, and molecular functions.

DML-Exon overlaps

Biological processes comparison

mrna-intron

Going forward

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