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), which contains the results of a comprehensive genome-wide in situ hybridization study of the adult mouse brain. ALLENMINER is an open-source program that searches the ABA for genes that (1) express, (2) express specifically, (3) express non-uniformly, or (4) express in a graded fashion in a user-specified region of interest.

Assessment of ALLENMINER enrichment queries by comparison to lists of genes manually curated from the ABA in situ data as enriched in 12 brain regions suggests a concordance of 95-99%. Comparison to regionally-enriched genes previously identified by microarray revealed a 60-80% concordance, in line with published genome-wide comparisons of ABA and microarray expression data.

In the accompanying manuscript, 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.

The ALLENMINER software package is freely available under the GPL v3 license. The current release (v 1.03) is available for download here: allenminer_v1.03.tar.gz. This package includes a users manual, also available here.

Several enrichment, patterning, and gradient queries are described in the accompanying manuscript. The commands used to run these queries, along with the input and output files, are available for download here: allenminer_manuscript_data.tar.gz (~290 MB).

The program requires Perl, Python, and the Bit::Vector module available at CPAN. The API released at the Allen Brain Atlas website has two files (AtlasAnnotation100.sva and brainstructures.csv) that are necessary to perform queries using the ABA brain structure names.

A script is provided to create a local mirror of the ABA expression files (.XPR and .XML) that requires the XML::Twig module available at CPAN.

PyMol or other PDB viewers are useful to visualize ROI partition definitions when performing a graded or patterning query.

A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas.
F. P. Davis, S. R. Eddy. Bioinformatics 2009. (local)