Question: Compare two lists of genes
0
gravatar for ruth
5.5 years ago by
ruth10
European Union
ruth10 wrote:

My problem: 

I have two lists of genes (genes of interest & background genes). I want to check if genes of interest are "enriched" for any disease or cellular pathway. My gene list was formed intersecting specific genome intervals with gencode.gtf (genes are in Ensembl ID).

What I tried:

I searched biostar and tried various suggestions (David, bioconductor packages). However I wasn't able to get David working and some bioconductor packages weren't available for my R version.

What I want:

Can I get suggestions what are you using (tools, R packages) for such analysis in 2014?

 

Thanks

 

 

gene set • 2.6k views
ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 5.5 years ago by ruth10
2

What do you mean by "not able to get David working"? David should work well for something like this.

ADD REPLYlink written 5.5 years ago by Devon Ryan94k

which bioconductor packages failed to install? Were you trying to use install.packages() or biocLite()?

ADD REPLYlink written 5.5 years ago by russhh5.2k

To add to russ_hyde 's comment, what version of R are you using that things weren't available?

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Devon Ryan94k

R version 3.0.1 (2013-05-16) -- "Good Sport"

ADD REPLYlink written 5.5 years ago by ruth10

There should be plenty of packages available in the older bioconductor repositories (remember that bioconductor packages aren't installed via install.packages()).

ADD REPLYlink written 5.5 years ago by Devon Ryan94k

Devon, what R packages do you recommend for such analysis?

ADD REPLYlink written 5.5 years ago by ruth10
1

David is fine, as is GOrilla as Manu just suggested. Anything like that will give essentially the same results.

ADD REPLYlink written 5.5 years ago by Devon Ryan94k
0
gravatar for Manvendra Singh
5.5 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

There is very nice web based tool which is getting cited too much, its called GOrilla.

http://cbl-gorilla.cs.technion.ac.il/

you can submit your gene (interest) list and background gene list. It would tell you about cellular pathways.

ADD COMMENTlink written 5.5 years ago by Manvendra Singh2.1k

I like Webgestalt since it offers many analysis options, not just GO

http://bioinfo.vanderbilt.edu/webgestalt/option.php

ADD REPLYlink written 5.5 years ago by roy.granit810
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