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Gene enrichment methods for Virginia DMRs #594

Closed yaaminiv closed 5 years ago

yaaminiv commented 5 years ago

I performed a gene enrichment in DAVID for DMR-mRNA overlaps, DML-mRNA overlaps, and flanking regions. The results can be found in this lab notebook entry. After correcting for multiple comparisons, there was only 1 significantly enriched term. I have two questions:

  1. @sr320, should I proceed with gene enrichments in DAVID for exon/intron/transposable elements given that there aren't many significantly enriched GOterms for mRNA overlaps? I'm going to start describing functions for the genes DMRs were found in, but wanted to know if I should focus more on descriptions or on both enrichment and descriptions.
  2. @laurahspencer, I know this was an issue you encountered with your quantseq stuff. What did you end up doing when you didn't have any significant comparisons after corrections?
yaaminiv commented 5 years ago

Decided not to focus on gene enrichment and instead look at gene product descriptions and comparison of hyper- and hypomethylated genes.