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Bioinformatics Advance Access originally published online on May 4, 2009
Bioinformatics 2009 25(13):1647-1654; doi:10.1093/bioinformatics/btp288
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas

Fred P. Davis * and Sean R. Eddy

HHMI Janelia Farm Research Campus, 19700 Helix Dr, Ashburn, VA 20147, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Gene expression patterns can be useful in understanding the structural organization of the brain and the regulatory logic that governs its myriad cell types. A particularly rich source of spatial expression data is the Allen Brain Atlas (ABA), a comprehensive genome-wide in situ hybridization study of the adult mouse brain. Here, we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned or graded in a user-specified region of interest.

Results: Regionally enriched genes identified by ALLENMINER accurately reflect the in situ data (95–99% concordance with manual curation) and compare with regional microarray studies as expected from previous comparisons (61–80% concordance). We demonstrate the utility of ALLENMINER by identifying genes that exhibit patterned expression in the caudoputamen and neocortex. We discuss general characteristics of gene expression in the mouse brain and the potential application of ALLENMINER to design strategies for specific genetic access to brain regions and cell types.

Availability: ALLENMINER is freely available on the Internet at http://research.janelia.org/davis/allenminer.

Contact: davisf{at}janelia.hhmi.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Olga Troyanskaya

Received on January 23, 2009; revised on April 9, 2009; accepted on April 24, 2009

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