ALLENMINER

ALLENMINER searches gene expression in the adult and developing mouse brain and spinal cord atlases published by the Allen Institute for Brain Science (AIBS). It can identify genes that are (1) expressed, (2) expressed specifically, (3) expressed non-uniformly, (4) expressed in a graded fashion, or (5) expressed in a pattern similar to a query gene, in a user-specified region of interest of the mouse brain -- specified either as a set of brain region names or as x,y,z bounds of a cuboid.

The code includes several routines for processing Allen Brain Atlas (ABA) data files, including the 3D expression data and the adult and developing reference atlases. Besides accessing the raw data, these routines are useful for visualizing ABA expression files on platforms where the ABA BrainExplorer application is not available, such as GNU/Linux. For example, all ABA expression files can be converted to PDB (protein data bank) format for visualization in protein structure viewers, such as PyMOL.

For more details take a look at the users manual for v2.0.

Easier to install. No longer requires Python, any CPAN packages, or the (now outdated) ABA API package.
Searches the latest atlases: ABA adult (v2.0; Nov 2011 release) and developing mouse brain atlases (v3.0; Nov 2011 release); adult and developing spinal cord atlases.
Easier to view results. Experimental mode (make_report) formats search results along with original 2D ISH images for viewing in a web browser.

Download ALLENMINER: allenminer_v2.0.tar.gz

External Software

The program requires four programs, usually installed on most machines: Perl, wget, unzip, and gzip.
Mac OS/X machines may not have wget by default, so check and download if necessary.

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

Citing ALLENMINER

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