Question: RNA-Seq Differential gene expression
0
gravatar for umeshtanwar2
18 months ago by
umeshtanwar230
umeshtanwar230 wrote:

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 • 357 views
ADD COMMENTlink modified 18 months ago by shawn.w.foley1.2k • written 18 months ago by umeshtanwar230

You can try ReactomePA

ADD REPLYlink written 18 months ago by Arup Ghosh2.8k

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

ADD REPLYlink written 18 months ago by umeshtanwar230
2
gravatar for WouterDeCoster
18 months ago by
Belgium
WouterDeCoster45k wrote:

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 COMMENTlink written 18 months ago by WouterDeCoster45k

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

ADD REPLYlink written 18 months ago by umeshtanwar230
2
gravatar for shawn.w.foley
18 months ago by
shawn.w.foley1.2k
USA
shawn.w.foley1.2k wrote:

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.

ADD COMMENTlink written 18 months ago by shawn.w.foley1.2k
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