Question

RNA-Seq Differential gene expression

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5.3 years ago

umeshtanwar2 ▴ 30

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

RNA-Seq • 1.4k views

ADD COMMENT • link updated 5.3 years ago by shawn.w.foley ★ 1.3k • written 5.3 years ago by umeshtanwar2 ▴ 30

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You can try ReactomePA

ADD REPLY • link 5.3 years ago by Arup Ghosh 3.2k

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

ADD REPLY • link 5.3 years ago by umeshtanwar2 ▴ 30

score 2 · Answer 1 · 2019-08-29

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5.3 years ago

WouterDeCoster 47k

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

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

So, you can't.

ADD COMMENT • link 5.3 years ago by WouterDeCoster 47k

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

ADD REPLY • link 5.3 years ago by umeshtanwar2 ▴ 30

score 2 · Answer 2 · 2019-08-29

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.