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Title: sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures
Authors: Zhang, Shu-Dong
Gant, Timothy W.
First Published: 31-Jul-2009
Publisher: BioMed Central Ltd
Citation: BMC Bioinformatics, 2009, 10:236
Abstract: Background: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. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures. Results:This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies. Conclusion:The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from webcite.
DOI Link: 10.1186/1471-2105-10-236
eISSN: 1471-2105
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright © 2009 Zhang and Gant; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Appears in Collections:Published Articles, MRC Toxicology Unit

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