Figure 1. Gene expression changes in autism cerebral cortex.
A. Heatmap of top 200 genes differentially expressed between autism and control cortex samples. Scaled expression values are color-coded according to the legend on the left. The dendrogram depicts hierarchical clustering based on the top 200 DE genes. The top bar (A/C) indicates the disease status: red-autism, black-control. The bottom bars show additional variables for each sample: sex (grey-male, black-female), brain area (black-temporal, grey-frontal), co-morbidity of seizures (green-autism case with seizure disorder, red-autism case without seizure disorder, black-control), age, RNA integrity number (RIN) and post mortem interval (PMI). The corresponding scale for quantitative variables is shown on the left.
B. Top: Venn diagram depicting the overlap between genes DE in frontal and temporal cortex. Bottom: Venn diagram describing the overlap between genes DE in the initial cohort (DS1) and the replication cohort (DS2). Differential expression in the initial cohort was assessed at an FDR<0.05 and fold changes>1.3. The statistical criteria were relaxed to p<0.05 for the replication dataset since it involved fewer samples.
C. Expression fold changes for all genes DE in the initial cohort are plotted on the x-axis against the fold changes for the same genes in the replication cohort on the y-axis. Green-genes downregulated in the autism group in both datasets, red-genes upregulated in the autism group in both datasets, grey-genes with opposite direction of variation in the two datasets. Horizontal lines show fold change threshold for significance.
D. (left) Diagram depicting the number of genes showing significant expression differences between frontal and temporal cortex in control samples (top) and autism samples (bottom) at FDR<0.05. (right) Top 20 genes differentially expressed between frontal and temporal cortex in control samples. All of the genes shown are also differentially expressed between frontal and temporal cortex in fetal midgestation brain10, but show no significant expression differences between frontal and temporal cortex in autism. The horizontal bars depict p values for differential expression between frontal and temporal cortex in the autism and control groups.