Question: Pathway enrichment analysis of gene set
1
gravatar for chipolino
23 months ago by
chipolino40
chipolino40 wrote:

Hi everyone,

I have list of genes (differentially expressed for example) and I want to obtain list of enriched pathways (not GO terms), what is the best tool or database to do it? Should I use KEGG or REACTOME database for this purpose or something else? I know, everyone has some preferences here, but I would like to hear opinion of someone who has a lot of experience in this field...

Thank you

ADD COMMENTlink modified 23 months ago by EagleEye6.6k • written 23 months ago by chipolino40
3
gravatar for Benn
23 months ago by
Benn8.0k
Netherlands
Benn8.0k wrote:

If you want to see which KEGG or REACTOME pathways are enriched in your list of genes, a simple approach is to use goseq. In the manual they explain how to do the enrichment analysis with custom (other than GO) databases such as KEGG or REACTOME. In my opinion, these results are always less informative than GO enrichment. The number of pathways are limited (compared to the number of GO terms), and GO terms may lead to novel insights (with pathways usually not).

ADD COMMENTlink written 23 months ago by Benn8.0k
0
gravatar for c.chakraborty
23 months ago by
c.chakraborty160
c.chakraborty160 wrote:

You can also upload your gene list to MSigDB and look for Pathway enrichment.

ADD COMMENTlink written 23 months ago by c.chakraborty160
0
gravatar for EagleEye
23 months ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

With GeneSCF batch run, you can try all those database with single run. Selecting the database depends on your experiment or study or interest.

KEGG always gives you broad perspective of pathway terms (metabolism, gene regulation, cellular processes, disease and signaling pathways).

In Gene Ontology, you can have individual terms in-detail like sub processes of these broad categories such as Biological Process (GO_BP), Molecular Function (GO_MF) and Cellular Component (GO_CC).

Reactome has database with sub-pathways of broad terms (broad terms as in KEGG). Reactome has advantage by covering more number of proteins.

More details in GeneSCF article.

ADD COMMENTlink modified 23 months ago • written 23 months ago by EagleEye6.6k
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