Table 3. The 72-member constrained gene subnetwork is preferentially expressed in a range of tissues and brain structures.
We find strong enrichment in a variety of tissues, predominantly neural and immune-derived samples sourced from the Roadmap Epigenome Project (REP) and the BrainSpan Atlas. We report only tissues passing significance with two conservative independent empirical approaches: random permutation of preferential expression values for the subnetwork across tissues (permutation); and comparison to the largest subnetworks detected when we permute constraint scores for all 9729 InWeb genes.
| Source | Tissue | Developmental stage | Permutation p-value | Resampled p-value | Tissue-specific genes |
|---|---|---|---|---|---|
| REP | CD34+ | Perinatal (cord blood) | 0.00100 | 0.00100 | 10 |
| REP | Fetal brain | Fetal | 0.01100 | 0.00100 | 16 |
| REP | CD8+ | Adult (>20 years) | 0.01700 | 0.00100 | 10 |
| REP | Fetal thymus | Fetal | 0.04800 | 0.00100 | 5 |
| BrainSpan | Caudal ganglionic eminence | 2A (8–9 pcw) | 0.00125 | 0.00125 | 20 |
| BrainSpan | Dorsolateral prefrontal cortex | 2A (8–9 pcw) | 0.00125 | 0.00125 | 16 |
| BrainSpan | Hippocampal anlage | 2A (8–9 pcw) | 0.00125 | 0.00125 | 17 |
| BrainSpan | Lateral ganglionic eminence | 2A (8–9 pcw) | 0.00125 | 0.00125 | 19 |
| BrainSpan | Primary motor-sensory cortex | 2A (8–9 pcw) | 0.00125 | 0.00125 | 20 |
| BrainSpan | Medial frontal cortex | 2A (8–9 pcw) | 0.00125 | 0.00125 | 19 |
| BrainSpan | Orbital frontal cortex | 2A (8–9 pcw) | 0.00250 | 0.00125 | 14 |
| BrainSpan | Parietal neocortex | 2A (8–9 pcw) | 0.00250 | 0.00125 | 18 |
| BrainSpan | Medial ganglionic eminence | 2A (8–9 pcw) | 0.00375 | 0.00125 | 18 |
| BrainSpan | Occipital neocortex | 2A (8–9 pcw) | 0.00500 | 0.00125 | 18 |
| BrainSpan | Hippocampus | 2B (10–12 pcw) | 0.00625 | 0.00125 | 18 |
| BrainSpan | Hippocampus | 3A (13–15 pcw) | 0.00625 | 0.00125 | 19 |
| BrainSpan | Primary somatosensory cortex | 3A (13–15 pcw) | 0.01250 | 0.00125 | 20 |
| BrainSpan | Primary visual cortex | 4 (19–24 pcw) | 0.01750 | 0.00125 | 22 |
| BrainSpan | Posterior superior temporal cortex | 3B (16–18 pcw) | 0.01875 | 0.00125 | 22 |
| BrainSpan | Posteroventral parietal cortex | 3A (13–15 pcw) | 0.02250 | 0.00125 | 19 |
| BrainSpan | Cerebellar cortex | 4 (19–24 pcw) | 0.02500 | 0.00125 | 19 |
| BrainSpan | Primary motor cortex | 3A (13–15 pcw) | 0.02750 | 0.00125 | 19 |
| BrainSpan | Striatum | 3A (13–15 pcw) | 0.04125 | 0.00125 | 17 |
| BrainSpan | Dorsolateral prefrontal cortex | 4A (19–24 pcw) | 0.04625 | 0.00250 | 21 |