RNA-Seq Differential gene expression

Question

[umeshtanwar2]

Hi all,

I am working on the RNAseq analysis in Arabidopsis plant. I have the list of DEGs which I obtained using DESeq2. I have done the annotation using biomaRt package. Now I would like to assign the DEGs to the Reactome pathways with graphical representation. Could you please help me in this?

Thansks

[Arup Ghosh]

You can try ReactomePA

[umeshtanwar2]

Thank you arup, but it does not support the plants.

Answer 1

[WouterDeCoster]

From the user guide: https://reactome.org/userguide

"Reactome is a curated database of pathways and reactions in human biology. "

So, you can't.

[umeshtanwar2]

Thank you WouterDeCoster. Is there any program/tool to assign the DEGs to the reactome or metabolic pathways in plants?

Answer 2

[shawn.w.foley]

AgriGO is a GO term enrichment resource developed for plant biologists, it has a straightforward userface and you can perform the analysis on their website. I used it frequently during my PhD, and highly recommend it.

If you're specifically interested in pathways rather than GO terms, you could try downloading the data from the Plant Metabolic Network (PMN). You can use the data with fGSEA or other gene set or GO enrichment analysis software to look for enrichments.