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Science. 2006 Sep 29;313(5795):1929-35.

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.

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  • 1Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.


To pursue a systematic approach to the discovery of functional connections among diseases, genetic perturbation, and drug action, we have created the first installment of a reference collection of gene-expression profiles from cultured human cells treated with bioactive small molecules, together with pattern-matching software to mine these data. We demonstrate that this "Connectivity Map" resource can be used to find connections among small molecules sharing a mechanism of action, chemicals and physiological processes, and diseases and drugs. These results indicate the feasibility of the approach and suggest the value of a large-scale community Connectivity Map project.

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