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sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

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posted on 2013-10-25, 09:37 authored by Shu-Dong Zhang, Timothy W. Gant
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 http://purl.oclc.org/NET/sscMap webcite.

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Citation

BMC Bioinformatics, 2009, 10:236

Version

  • VoR (Version of Record)

Published in

BMC Bioinformatics

Publisher

BioMed Central Ltd

eissn

1471-2105

Copyright date

2009

Available date

2013-10-25

Publisher version

http://www.biomedcentral.com/1471-2105/10/236

Language

en

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