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

  • Authors:

  • Amira Djebbari;Svetlana Karamycheva;Eleanor Howe;John Quackenbush

  • Affiliations:

  • The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA;The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA;Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute Boston, MA, USA;The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA

  • Venue:
  • Bioinformatics
  • Year:
  • 2005

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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 Contact: johnq@jimmy.harvard.edu Supplementary information: Results from the analysis of significant genes from the published Ang II study.