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Bioinformatics Advance Access published online on May 26, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti503
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received April 4, 2005
Revised May 15, 2005
Accepted May 16, 2005

Applications note

MeSHer: identifying biological concepts in microarray assays based on PubMed references and MESH terms

Amira Djebbari 1, Svetlana Karamycheva 2, Eleanor Howe 3, and John Quackenbush 4*

1 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850; Department of Computer Science, The George Washington University, Washington, DC, USA
2 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850
3 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
4 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850; Department of Biochemistry, The George Washington University, Washington, DC, USA; Department of Statistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA

* To whom correspondence should be addressed.
John Quackenbush, E-mail: johnq{at}jimmy.harvard.edu


  Abstract

Summary: MeSHer uses a simple statistical approach to identify biological concepts in the form of Medical Subject Headings (MeSH terms) obtained from the PubMed database that are significantly overrepresented within the identified gene set relative to those associated with the overall collection of genes on the underlying DNA microarray platform. As a demonstration, we apply this approach to gene lists acquired from a published study of the effects of angiotensin II (Ang II) treatment on cardiac gene expression and demonstrate that this approach can aid in the interpretation of the resulting "significant" gene set.

Availability: The software is available at http://www.tm4.org.

Supplementary information: Results from analysis of significant genes from the published Angiotensis II study.


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