Table 2.
Resources for expression-related validation of single nucleotide polymorphisms (eQTL) and gene sets in tissue from the central nervous system
| Source | Brain Tissue type | dbGaP or other accession points | URL for online queries |
|---|---|---|---|
| GTEx | Anterior cingulate cortex (n = 72), caudate (n = 100), cerebellar hemisphere (n = 89), cerebellum (n = 103), cortex (n = 96), frontal cortex (n = 92), hippocampus (n = 81), hypothalamus (n = 81), nucleus accumbens (n = 92), putamen (n = 82) | phs000424.v6.p1 | http://www.gtexportal.org/home/ |
| BRAINEAC | Cerebellum, frontal cortex, hippocampus, medulla, occipital cortex, putamen, substantia nigra, thalamus, intralobular white matter, temporal cortex (n = 134) | - | http://www.braineac.org/ |
| CommonMind | Dorsolateral prefrontal cortex (n = 291 control, 275 SCZ, 47 BIP) |
https://www.nimhgenetics.org/available_data/commonmind/ https://www.synapse.org/#!Synapse:syn2759792/wiki/197295 |
|
| Braincloud | Prefrontal cortex (14 weeks to 80 years, n = 269) | phs000417.v2.p1 | http://braincloud.jhmi.edu/downloads.htm |
| Meta-analysis of eQTL data | Cortical samples from 5 studies (n = 424) | Significant SNP – gene pair associations in supplement of http://www.nature.com/tp/journal/v4/n10/full/tp201496a.html | |
| PsychENCODE | dorsolateral prefrontal cortex, anterior cingulate cortex, inferior temporal cortex, hippocampus, amygdala, caudate nucleus, nucleus accumbens and cerebellar cortex (n = 1,000 including control and disease-related) | https://www.synapse.org//#!Synapse:syn4921369/wiki/390660 | |
| DNA Methylation and expression in human brain | Cerebellum, frontal cortex, pons, and temporal cortex (n = 382) | phs000249.v2.p1 | - |
| Gene network | Multiple tissues spanning humans, mice (BXD, AXB, LXS, etc.), rats (HXB), and drosophila. | http://genenetwork.org/webqtl/main.py | |