Figure 4.

Enrichment of MED Gene Expression Signature with ASD-Related Genes, Biological Pathways, and Spatiotemporal Analysis

To interpret the broad biological relevance of MED and ASD expression signatures, differentially expressed genes before FDR correction were further analyzed.

(A) The MED (black) and ASD (gray) differentially expressed genes were tested for enrichment in five lists: (1) highly brain-expressed genes, (2) putative ASD risk genes, (3) gold standard ASD risk genes, and (4) highly liver-expressed genes (negative control). Significance was tested using the binomial test with a cutoff of p = 0.05 (red line). Both ASD and MED genes were enriched in brain, Princeton, and SFARI lists, although the effect size of the MED signature was notably stronger. Neither set overlapped with liver-expressed genes, a negative control.

(B) Biological processes implicated with MED. The gene expression signature of MED affects neurodevelopmental, cell migration, and growth-related ontologies. Significance of enrichment was calculated using Fisher's exact test with false discovery rate control and a cutoff of p_FDR = 0.05 (red line).

(C) Gene lists from 16 neuroanatomical regions and 13 developmental stages were tested for enrichment with the MED genes. The neuroanatomical regions include the inferior temporal cortex (ITC), thalamus (THA), dorsal frontal cortex (DFC), medial frontal cortex (MFC), cerebellar cortex (CB), ventral frontal cortex (VFC), hippocampus (HIP), superior temporal cortex (STC), primary visual cortex (V1C), amygdala (AMY), inferior parietal cortex (IPC), primary auditory cortex (A1C), striatum (STR), primary motor cortex (M1C), olfactory cortex (OFC), and primary somatosensory cortex (S1C). Fisher's exact test was performed for each region-stage pair and plotted on a heatmap after false discovery rate correction. A variety of cortical and deeper structures are implicated in MED, primarily at prenatal time points. Strong enrichment of the DFC and MFC is also indicated during late childhood. The grayed-out regions represent structures that are not present in the early prenatal brain.

(D) Visualization of cortical and interior MED-associated regions during late prenatal development (25–28 post conceptual weeks). Raw enrichment p values (p_raw) were plotted to show the range of structural involvement at this time point. Cortical regions such as the A1C, S1C, and ITC are enriched for the MED signature; however, deeper lying structures such as the thalamus and striatum are also revealed.