GO terms and Venn Diagrams

Obtaining GO IDs My analysis prior to this used DESeq2 to obtain a series of tables of genes with significantly-different expressions for each of my four comparisons. I wrote a script in R that took in each DESeq2 output file, matched it against this annotated transcriptome, and produced a newline-separated file of UniProt accessions. I then took each newline-separated file and put it into this Bash script from Sam, which retrieved the Gene Ontology terms for each Accession ID. This is progressing fairly well! Next steps are as follows: Get the GOslim terms using the GSEAbase package Perform gene enrichment analysis with TopGO or GO-MWU When time allows, go back and annotate the transcriptome myself to understand it more fully Producing Venn Diagrams In order to determine the overlap between DEGs for my different comparisons, I produced a few Venn diagrams. Since a quick analysis found practically no overlap between…

from Aidan F. Coyle https://ift.tt/3hcKQof
via IFTTT