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Bioinformatics Shared Resources

Sanford Burnham Prebys Medical Discovery Institute

cancer-genomics

CANCER GENOMICS & DATASETS

Useful global datasets focusing on Cancer.

1. The Global Cancer Map

Multiclass cancer diagnosis using tumor gene expression signatures

Sridhar Ramaswamy*,dagger , Pablo Tamayo*, Ryan Rifkin*,Dagger , Sayan Mukherjee*,Dagger , Chen-Hsiang Yeang*,§, Michael Angelo*, Christine Ladd*, Michael Reich*, Eva Latulippe, Jill P. Mesirov*,Tomaso PoggioDagger , William Gerald, Massimo Lodadagger ,||, Eric S. Lander*,**, and Todd R. Golub*,dagger dagger ,DaggerDagger

This is a Human 190 chip data set showing differential gene expression between a wide variety of different tumour types. The experiment was carried out using affymetrix arrays. The raw data is available here: http://www.pnas.org/cgi/content/full/98/26/15149

If you would like to see which genes are co-expressed with a gene that is particularly interesting to you ("guilt by association") the dataset has been clustered using Hierarchical clustering and is available for down load here:

Clustered Global Cancer Map  Download
To view the results and search for genes you will need to small free TREEVIEW Viewer available here: http://rana.lbl.gov/EisenSoftware.htm 

Once you have unzipped and run this program,  use it to load the file: GCM_Total.preprocessed.cdt from the cluster download.
Tumors only Global Cancer Map  Download