Transcriptomic and Epigenetic Findings in Autism Figure 2. Specific domains of the Autism Diagnostic Interview-Revised (ADI-R) are associated with specific gene modules. (A) Heatmap of module-variable associations for cerebellar hemisphere samples from weighted genome co-expression network analysis, including domain scores for the ADI-R. Cells are color-coded by correlation coefficient and * is placed in cells having associations with p-values #0.01. Autism, dichotomous variable autism vs control; PMI, postmortem interval; A, ADI-R Social interaction impairments domain; B, ADI-R Communication and language impairments domain; C, ADI-R Repetitive and stereotyped behaviors domain. (B) Gene ontology enrichment annotation clusters for the three significant gene modules associated with specific ADI-R domain scores. P, p-value; r, Pearson correlation coefficient. doi:10.1371/journal.pone.0044736.g002 procure brain specimens from numerous persons with autism, particularly after stringent selection criteria are used. Second, as is the case for any study, we cannot exclude that our results are artifacts of an unmeasured covariate. However, we tried to exclude potential confounders by exploring postmortem interval, cause of death, seizure comorbidity and age, as well as tissue variables such as RNA quality and tissue sampling error. Third, although we had excellent genomic coverage on both our methylation and gene expression arrays, we did not have complete coverage and we may have missed small epigenomic or transcriptional changes with pathologic relevance. We did not evaluate histone modifications, which can account for expression differences in the absence of differential DNA methylation. Fourth, we evaluated two carefully chosen brain regions but in so doing may have missed important gene expression or DNA methylation changes in other brain regions. PLOS ONE | www.plosone.org 6 September 2012 | Volume 7 | Issue 9 | e44736