GSEA analysis

[48sh...@cua.edu]

Hi,

I have RNA seq data analysed. I have set of genes which are differentially regulated in two set of samples. I want to use GSEA to pull down all ER alpha target genes. Is it possible to use this software. or I can get information of what ER targets are. Please let me know is that application possible using GSEA. if yes can you provide me some guidance.

Thanking You

[PABLO TAMAYO]

Yes, you can run GSEA analysis with gene sets from the Molecular Signatures database (msigdb.org) and see if gene sets such as:

HALLMARK_ESTROGEN_RESPONSE_EARLY

HALLMARK_ESTROGEN_RESPONSE_LATE

GO_ESTROGEN_RECEPTOR_BINDING

STEIN_ESR1_TARGETS

STEIN_ESRRA_TARGETS

STEIN_ESRRA_TARGETS_DN

STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_DN

STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP

STEIN_ESRRA_TARGETS_UP

STEIN_ESTROGEN_RESPONSE_NOT_VIA_ESRRA

STOSSI_RESPONSE_TO_ESTRADIOL

etc...

are enriched in your differentially expressed genes.

--Pablo

___________________________________________________________

Dr. Pablo Tamayo (pta...@ucsd.edu)

Director, UCSD Center for Cancer Target Discovery and Development (CTD2)

Group Leader, Computational Cancer Analysis Laboratory (CCAL)

Co-Director, Genomics and Computational Biology Shared Resource (GCBSR)

Professor, Division of Medical Genetics, UC San Diego School of Medicine

UC San Diego Moores Cancer Center (Room 3017)

3855 Health Sciences Drive MC 0658, La Jolla, CA  92093-0658

Visiting Scientist, Cancer Program, Broad Institute of MIT/Harvard

___________________________________________________________

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/ee83977e-ddd3-4549-8407-93432780b59e%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[David Eby]

Note that we recommend running GSEA with expression data from the full genome instead of a filtered list of just the differentially expressed genes.  Using a reduced list can blunt the statistical power of the GSEA method.  Also, it may be necessary to use our new Ensembl CHIP files to collapse / convert into HUGO symbols to run against the provided MsigDB gene sets.

We also suggest starting with the Hallmarks collection to get an overview before drilling into more specific collections.

As an alternative if you don't have the expression data and only have the filtered gene list, you can try the Compute Overlaps tool on our website.  This is a much simpler pathway analysis but may still provide useful results.

Regards,

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org