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Here, we surveyed bioinformatics software tools for exploring gene expression connectivity mapping. Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database.
(Zhang and Gant 2009) sscMap: an extensible Java application for connecting small-molecule drugs using gene-expression signatures. BMC Bioinformatics.