Question: GSEA mouse sets
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gravatar for kanwarjag
2.6 years ago by
kanwarjag950
United States
kanwarjag950 wrote:

I am looking for a resource to download MSIG db C2CGP and C7 homologues of mouse. http://software.broadinstitute.org/gsea/downloads.jsp has human genes but I am looking for mouse dataset. I understand I can compile it by homologous search, but want to see if pre compiled list is available at some source. Thanks

rna-seq • 6.8k views
ADD COMMENTlink modified 2.6 years ago by natasha.sernova3.4k • written 2.6 years ago by kanwarjag950
2
gravatar for natasha.sernova
2.6 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

See this post:

GSEA analysis with Mouse (Please give some comments..)

And these paper:

https://www.bioconductor.org/packages/release/data/experiment/vignettes/gskb/inst/doc/gskb.pdf

And these tools: this one:

http://www.bioinformatics.org/go2msig/

And this one:

http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ

"What array platforms and organism species does GSEA support?

GSEA works on any data, as long as the gene identifiers in your expression data match those in the gene sets file.

Typically, GSEA uses gene sets from MSigDB. All gene sets in MSigDB consist of human gene symbols. GSEA has build-in tools for conversion between a variety of other gene identifiers to human gene symbols by means of specially formatted CHIP files. The CHIP files provide the mapping between gene identifiers in your expression data and gene identifiers in the gene sets. Specifically, our CHIP files provide the mappings from all kinds of different platforms (e.g., mouse Affymetrix probe set IDs, human Affymetrix probe set IDs, etc.) to human gene symbols.

If your data was generated from non-human samples, then you need to decide whether using MSigDB meets your needs. The options are:

The non-human species serves as a model to study conditions relevant for human biology. In this case, you want gene sets that are conserved between humans and your model organism. MSigDB is then the right choice and you will only need to provide the appropriate CHIP file for the analysis.
The non-human species is the subject of your research, and you have no plans to compare it to human gene sets. In this case, you can still use MSigDB is your organism is among the sources of some of MSigDB gene sets (e.g., mouse or rat) and you will only need to provide the appropriate CHIP file for the analysis.
The non-human species is the subject of your research and you don't want to use MSigDB gene sets for other reasons. In this case, you have to provide your own database of gene sets as a GMT or GMX file. The file formats are described here. Of course, you still have to make sure that the gene identifiers in your your data match those in your gene sets database. If the identifiers don't match each other, then you have to also provide a CHIP file with the appropriate mappings. The CHIP file format is described here.

To see what CHIP files are available in our distribution (note: our CHIP files provide mappings to human gene symbols only): start GSEA desktop application and click [...] at "Chip platform(s)" on "Run GSEA" page."

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by natasha.sernova3.4k
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