Document Type


Publication Date




Publication Title

Brain Informatics






Recent studies have shown that projection targets in the mouse neocortex are correlated with their gene expression patterns. However, a brain-wide quantitative analysis of the relationship between voxel genetic composition and their projection targets is lacking to date. Here we extended those studies to perform a global, integrative analysis of gene expression and projection target correlations in the mouse brain. By using the Allen Brain Atlas data, we analyzed the relationship between gene expression and projection targets. We first visualized and clustered the two data sets separately and showed that they both exhibit strong spatial autocorrelation. Building upon this initial analysis, we conducted an integrative correlation analysis of the two data sets while correcting for their spatial autocorrelation. This resulted in a correlation of 0.19 with significant p value. We further identified the top genes responsible for this correlation using two greedy gene ranking techniques. Using only the top genes identified by those techniques, we recomputed the correlation between these two data sets. This led to correlation values up to 0.49 with significant p values. Our results illustrated that although the target specificity of neurons is in fact complex and diverse, yet they are strongly affected by their genetic and molecular compositions.


© 2015 The Authors.

Published under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits any use, distribution, and reproduction in any medium, provided the original authors and the source are credited.

Original Publication Citation

Fakhry, A., Zeng, T., Peng, H., & Ji, S. (2015). Global analysis of gene expression and projection target correlations in the mouse brain. Brain Informatics, 2(2), 107-117.


0000-0002-4205-4563 (Ji)