Where Can I Find Additional Gene Sets To Extend Msigdb For Gsea?

Question

[enricoferrero]

Hi everyone,

I am looking for additional gene sets that can be used to expand the gene sets found in the Molecular Signatures Database (MSigDB). In particular, I am looking for signatures such as the c6 (oncogenic signatures) and c7 (immunologic signatures) gene sets, i.e.: lists of genes up and downregulated across different conditions from a diverse panel of gene expression experiments (micorarray, RNA-seq).

The idea is to then run GSEA using this expanded collection of gene sets and hopefully get some biological insights about the datasets I'm analysing. Ideally, these gene sets would already be in GMT format, but I'm obviously flexible about this.

Hasn't anybody attempted to analyse all of GEO using some fixed thresholds and made a database yet? :)

Thanks very much!

Answer 1

[Charles Warden]

I actually developed an algorithm called BD-Func to compare up-regulated versus down-regulated gene expression. The package includes MSigDB listings for MSigDB (although I should add the c7 signatures) and GO (positive regulation of X, negative regulation of X).

You can download the GO gene lists along with the main package:

http://sourceforge.net/projects/bdfunc/

There are also 3 additional signatures specifically defined by BD-Func:

http://sourceforge.net/p/bdfunc/discussion/signatures/

I'll have to check out those links that you provided, but I didn't see a direct link to the positive/negative regulation GO gene lists.

[farhad.maleki.ca]

What do you mean by "positive/negative regulation gene lists"; do you mean gene sets where we have information about up-regulation or down-regulation of their genes?

[Charles Warden]

Up- and Down-regulation here refers to the pathway (as indicated from gene expression changes in other experiments).

Let's say the pathway is Notch signaling. "UP" would be the downstream targets that are activated and "DOWN" would be the downstream targets that are repressed. Or, if the gene list is associated with a drug treatment, it would be the genes with increased expression due to drug treatment versus genes with decreased expression due to drug treatment.

[farhad.maleki.ca]

Thanks Charles, that would definitely be useful to have information about Up- and Down-regulation of genes within a gene set. The available gene set databases, such as MSigDB, do not provide any information about Up- and Down-regulation. Do you know how can I get such information about gene sets?

[Charles Warden]

It is in the names of the signatures from MSigDB.

For example, when NOTCH is inhibited by DAPT, these are the up-regulated genes:

http://software.broadinstitute.org/gsea/msigdb/cards/NOTCH_DN.V1_UP

and these are the down-regulated genes:

http://software.broadinstitute.org/gsea/msigdb/cards/NOTCH_DN.V1_DN

In this case, the nomenclature is a little confusing

Answer 2

[enricoferrero]

Here's what I've found so far:

GeneSetDB (PubMed)

GeneSigDB (PubMed)

PAGED (PubMed)

Enriched Maps Gene Sets (PubMed)

[farhad.maleki.ca]

Would you please et me know if I can get PAGED database (I mean the whole database)