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):


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:


And here it is with the gene panel only:


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.

About bgeedb

This is the blog of the database of gene expression evolution Bgee, at University of Lausanne and Swiss Institute of Bioinformatics.
This entry was posted in topanat, using bgee and tagged , , , . Bookmark the permalink.

1 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

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s