Question: GO Term Analysis
0
gravatar for pthom010
3 months ago by
pthom0100
pthom0100 wrote:

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).

annotation go rna-seq R • 214 views
ADD COMMENTlink written 3 months ago by pthom0100
2

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 REPLYlink written 3 months ago by ATpoint44k

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 REPLYlink modified 12 weeks ago • written 12 weeks ago by pthom0100
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