Compare two lists of genes

Question

[ruth]

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

[Devon Ryan]

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

[russhh]

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

[Devon Ryan]

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

[ruth]

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

[Devon Ryan]

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

[ruth]

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

[Devon Ryan]

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

Answer 1

[Manvendra Singh]

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

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

[roy.granit]

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

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