Supplement to Relationships between gene expression and brain wiring in the adult rodent brain.
French L, Pavlidis P 
PLoS computational biology 2011 Jan 6;7(1):e1001049
Abstract
We studied the global relationship between gene expression and neuroanatomical connectivity in the adult rodent brain. We utilized a large data set of the rat brain “connectome” from the Brain Architecture Management System (942 brain regions and over 5000 connections) and used statistical approaches to relate the data to the gene expression signatures of 17,530 genes in 142 anatomical regions from the Allen Brain Atlas. Our analysis shows that adult gene expression signatures have a statistically significant relationship to connectivity. In particular, brain regions that have similar expression profiles tend to have similar connectivity profiles, and this effect is not entirely attributable to spatial correlations. In addition, brain regions which are connected have more similar expression patterns. Using a simple optimization approach, we identified a set of genes most correlated with neuroanatomical connectivity, and find that this set of genes is enriched for genes involved in neuronal development and axon guidance. A number of the genes have been implicated in neurodevelopmental disorders such as autistic spectrum disorder. Our results have the potential to shed light on the role of gene expression patterns in influencing neuronal activity and connectivity, with potential applications to our understanding of brain disorders. Supplementary data are available at http://www.chibi.ubc.ca/ABAMS.
Contact
paul@msl.ubc.ca
leonfrench@gmail.com
Updates
Update – source code available at github.
Update – connection and nomenclature matrices added below.
Update – we have published a related analysis in Frontiers in Neuroinformatics.
Presentation
The file “gene-lists-supplement-brain-wiring.txt” is formated for the Venn Master software tool.
The Dong.CA1 sets are from “Genomic-anatomic evidence for distinct functional domains in hippocampal field CA1” by Dong et al.
The Top1000 Validation sets are from “The Allen Brain Atlas: 5 years and beyond” by Jones et al.
The AutismDB set is from AutDB.
-Full BAMS connection matrix from Swanson 1998 data
-Full BAMS connection matrix from Swanson 1998 data, up propigated
The above matrices are directed (962 by 962 regions) and derived from the RDF converted Swanson-98.xml file by John Barkley. Updated connectivity data can be found at the Brain Architecture Management system (BAMS). If a row and column pair is a 1 in these full matrices then there is a reported BAMS connection from the row-region (source) to the column-region (target).