Confirming that autism and epilepsy genes are expressed in specific brain areas

Recently we presented on this blog a quick-and-dirty analysis of genes with the keyword “autism” from the GWAS Catalog at EBI. But recently, Jabbari and Nürnberg have published a more thorough study of autism and epilepsy candidate genes:

Jabbari and Nürnberg 2016 A genomic view on epilepsy and autism candidate genes Genomics doi:10.1016/j.ygeno.2016.01.001

The supplementary data of this paper provides a list of candidate genes from ClinVar, exome sequencing, and a gene panel from Lemke et al.

Analyzing all their genes in TopAnat, we get clear enrichment for specific brain substructures (as always, click on images to go to original results):

epilepsy_autism1

In Jabbari and Nürnberg they discuss differences in GO enrichment between the Lemke genes and the exome+ClinVar. What of anatomical structure enrichment?

Here is the enrichment with exome+ClinVar only:

epilepsy_autism2

And here it is with the gene panel only:

epilepsy_autism3

Seven of the top 20 are in common: nucleus accumbens, hypothalamus, superior frontal gyrus, dorsolateral prefrontal cortex, caudate nucleus, putamen and spinal cord. And most others are found lower ranked. Overall, less than 20% of the anatomical terms found with ClinVar + exome are not found with the gene panel, at an FDR of 20%. Thus, the two approaches yield extremely similar gene lists in terms of their expression patterns. Which is reassuring.

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About bgeedb

This is the blog of the database of gene expression evolution Bgee, at University of Lausanne and Swiss Institute of Bioinformatics. http://www.bgee.org/
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One Response to Confirming that autism and epilepsy genes are expressed in specific brain areas

  1. Pingback: When fold-enrichment is more informative than p-values: #TopAnat analysis of autism genes from GWAS | bgeedb

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