Table 1.
Overlaps and differences between CMC and other publicly available eQTL resources
| Comparison cohort eQTL genes compared to CMC eQTL |
||||||||
|---|---|---|---|---|---|---|---|---|
| Cohort | Sample Size | Study PMID/GEO ID/dbGaP ID |
Number of cis eQTL |
Proportion of non-null hypotheses (π1) in CMC |
Unique Genes with eQTL |
eQTL Genes Expressed in CMC |
Genes with eQTL in CMC |
Genes w/ eQTL in CMC but not in comparison cohort |
| Blood eQTL | 2494 twins | 24728292 | 9640* | 0.54 | 9533 | 8108 | 6794 | 5052 |
| Brain Cloud | 108 | GSE30272 | 374223 | 0.7 | 6199 | 5386 | 4666 | 7180 |
| Brain Meta- analysis |
424 | 25290266 | 3520** | 0.62 | 3503 | 2806 | 2507 | 9339 |
| GTEx PFC | 92 | 25954002 | 173026 | 0.98 | 1922 | 1326 | 1284 | 11853 |
| HBCC | 279 | phs000979.v1.p1 | 788338 | 0.77 | 7514 | 6785 | 5862 | 7275 |
| HBTRC | 146 | GSE44772 | 531400 | 0.75 | 6473 | 5186 | 4555 | 7291 |
| NIM | 145 | GSE15745 | 105735 | 0.79 | 2127 | 2057 | 1851 | 9995 |
| UKBEC | 134 | 25174004 | 52593 | 0.93 | 808 | 618 | 546 | 11300 |
| UNION | 1573706 | 0.7 | 16568 | 12644 | 10544 | 2593 | ||
*
Best eQTL per probeset reported
**
Best eQTL per gene reported
FDR ≤ 5% used to define eQTL in all cohorts. eQTL for Brain Cloud, HBCC, HBTRC, NIH and UKBEC were computed as described in the supplement. eQTL for the Blood cohort, Brain Meta-analysis and GTEx were downloaded from public resources. All eQTL resources represent prefrontal or frontal cortex except the Blood cohort (peripheral blood) and the Brain Meta-analysis (meta-analysis across multiple brain regions). The UNION set was derived by including all unique eQTL from all 8 cohorts.