Nature research paper: Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD
To identify differentially expressed genes and transcripts between all 55 pairs of cortical regions with our permutation-based approach, a regressed gene-expression dataset containing only the random effect of subject and the fixed effects of diagnosis and region was used.
The previously described permutation approach was designed to identify differences in transcriptomic regional identity in ASD. Importantly, this method is not appropriate for assessing variance in expected numbers of differentially expressed genes between regions across regional pairs and diagnoses, since the number of ASD and control subjects varied across regional pairs. To examine this, we also implemented a bootstrap-based approach.
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