GO Term Analysis

0

Entering edit mode

4.1 years ago

pthom010 ▴ 40

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).

R rna-seq go annotation • 987 views

ADD COMMENT • link 4.1 years ago by pthom010 ▴ 40

2

Entering edit mode

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.

ADD REPLY • link 4.1 years ago by ATpoint 85k

0

Entering edit mode

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!

ADD REPLY • link 4.1 years ago by pthom010 ▴ 40

Login before adding your answer.