Connectivity Map (cmap)

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract The Connectivity Map (also known as cmap) is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern- matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes.

It is designed to allow biologists, pharmacologists, chemists and clinical scientists to use cmap without the need for any specialist ability in the analysis of gene-expression data.

Note: While the ultimate goal of biomedicine is to connect each human disease with drugs that can effectively treat or cure it, the paths toward this goal are often circuitous. The earliest steps, in particular, can be hindered by a lack of basic knowledge about how drugs and diseases work - for example, the biology that underlies a particular disease or the molecules that are targeted by a drug’s action.

What is needed to accelerate this match-making process is a relatively quick and systematic method for comparing different drugs and diseases based on their biological effects.

Toward this end, a research team led by Broad Institute scientists has developed the cmap tool that relies on genes to connect diseases with potential drugs to treat them and to predict how new drugs function in cells.

To build the Connectivity Map, the scientists described the effects of different drugs and diseases using the common language of "genomic signatures" - the full complement of genes that are turned on and off by a particular drug or disease.

The scientists compiled the genomic signatures of more than 160 drugs and other biologically active compounds, forming a database of biological "barcodes" that denote cells' responses to the different drugs.

Then, they developed a computer program (cmap) that matches the barcodes based on the patterns shared among them. Together, these features enable the Connectivity Map to directly compare the biological effects of different drugs with each other, and also with those seen in diseases.

The Connectivity Map can be queried by nearly any researcher with a computer, where the search "word" is the genomic signature of a particular human disease, drug or other biological response of interest, and the search results consist of a rank-ordered list of reference compounds that have matching signatures.

These comparisons can yield new scientific insights, particularly when a connection exists between a poorly understood drug (or disease) and a drug whose effects have been extensively characterized - the case for many of the compounds currently referenced in the database.

This potential is underscored by two (2) cases where the Connectivity Map has already been used: one, to discover the mechanisms underlying a novel drug candidate for prostate cancer and another, to reveal that a drug currently used to treat one disease may be useful in another.

A web interface provides access to the current version (build 02) of Connectivity Map which contains more than 7,000 expression profiles representing 1,309 compounds.

Previous version (build 01) of the Connectivity Map.

You can learn more about cmap from the following Science paper:

The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease -- Science 29 September 2006: Vol. 313. no. 5795, pp. 1929 - 1935 DOI: 10.1126/science.1132939

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site Connectivity Map (cmap)

Price Contact manufacturer.

G6G Abstract Number 20203

G6G Manufacturer Number 101795