Question: Pathway Enrichment & Genes Shared Between The Pathways
4
gravatar for Dataminer
7.4 years ago by
Dataminer2.7k
Netherlands
Dataminer2.7k wrote:

Hi!

This is extension of the thread related to pathway enrichment tools discussed previously and quite extensively here on Biostars.

I have little complicated question:

Imagine you have a list of genes (more than 1000) and you want to know the pathways that are enriched by them (with p value <0.05) and also the number of genes shared between these pathways.

Any ideas to do this in less time consuming & efficient manner?

Thank you

enrichment R • 3.7k views
ADD COMMENTlink modified 7.3 years ago by lkmklsmn930 • written 7.4 years ago by Dataminer2.7k

Maybe you could link the previous thread here so people know what you are talking about ;-)

ADD REPLYlink written 7.4 years ago by Michael Schubert7.0k

"Reactome" would be a good answer ?

ADD REPLYlink written 7.4 years ago by justinhaselbach250
5
gravatar for Giovanni M Dall'Olio
7.4 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

I like very much the list of tools posted here:

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Giovanni M Dall'Olio27k
4
gravatar for luigra
7.4 years ago by
luigra40
luigra40 wrote:

Hi, we recently developed FIDEA a tool thought to facilitate the enrichment analysis. You can find it at http://www.biocomputing.it/fidea If you think that it is useful for your purpose and/or you need help let me know.

ADD COMMENTlink modified 7.4 years ago by Giovanni M Dall'Olio27k • written 7.4 years ago by luigra40
2
gravatar for enunvillafer
7.4 years ago by
enunvillafer100
Cuba
enunvillafer100 wrote:

Hi, have you used the modular enrichment analysis of DAVID?

ADD COMMENTlink written 7.4 years ago by enunvillafer100
2
gravatar for ewre
7.4 years ago by
ewre220
United States
ewre220 wrote:

DAVID and webgastalt would be your choice

ADD COMMENTlink written 7.4 years ago by ewre220
2
gravatar for Richard Smith
7.4 years ago by
Richard Smith400
Cambridge, UK
Richard Smith400 wrote:

You can also see pathway enrichment at the various InterMine sites, e.g for human genes you can upload a list at metabolicMine: http://metabolicmine.org/beta/bag.do, for fly use FlyMine: http://www.flymine.org/query/bag.do.

I think you can also do enrichment calculations via the API.

ADD COMMENTlink written 7.4 years ago by Richard Smith400
1
gravatar for Alex Paciorkowski
7.3 years ago by
Rochester, NY USA
Alex Paciorkowski3.4k wrote:

I now use this: Lynx developed at the Computation Institute at the University of Chicago. It includes a network based prioritization algorithm here. You can batch upload big lists of genes. I haven't done 1000 yet, but I bet you probably could. Plus, they have a web service.

ADD COMMENTlink written 7.3 years ago by Alex Paciorkowski3.4k

Good one :) Thank you

ADD REPLYlink written 7.3 years ago by Dataminer2.7k
1
gravatar for lkmklsmn
7.3 years ago by
lkmklsmn930
United States
lkmklsmn930 wrote:

I usually download the pathway annotation system and then convert it into an adjacency matrix. Using Fisher's Exact test you can then easily determine significance of gene set overlaps!

ADD COMMENTlink written 7.3 years ago by lkmklsmn930
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