GO Term Analysis
I am conducting an RNA seq analysis in R using DESeq2. I have a few sets of differentially expressed genes from a de novo organism and have the TAIR equivalents. I was wondering if there is a program in R/R Studio I can use to do GO term enrichment analysis with the TAIR locus ID numbers (or the nucleotide FASTA files if feasible).
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pthom010 •
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gprofiler2 can do GO term (and others such as REACTOME and KEGG) analysis using gene names as start. You should use all genes that are non-NA in the padj field as background, see https://biit.cs.ut.ee/gprofiler/gost. It also has an R package over at CRAN. You need gene names though, not coordinates or sequences.
Thanks. A bit confused on the padj point. I was looking on the gprofiler page and don't see anywhere to input background genes. I have a set of differentially expressed TFs clustered into groups. Would you recommend my background be all TFs that are non NA or just all non NA genes? Thanks for the recommendation!