GWAS genes | Response genes |
---|
 |  | Hard threshold | Lenient threshold | No threshold | All genes |
---|
TF | Regulon size | # Hit | FDR | # Hit | FDR | # Hit | FDR | # Hit |
P-value
| FDR |
---|
IRF1
| 318 |
10 (1.5)
| 2.9 1e−07 |
34 (12.5)
| 2.0 1e−07 |
83 (60)
| 0.07 |
37 (11.5)
| 5.19 1e−11 | 7.67 1e−08 |
CIITA
| 372 |
9 (1.5)
| 2.4e−08 |
26 (13)
| 0.08 |
83 (69)
| 1 |
45 (13.2)
| 1.31 1e−13 | 1.96 1e−10 |
SPIB
| 174 |
6 (0.5)
| 2.9e−04 |
14 (5.8)
| 0.6 |
43 (30.7)
| 1 |
14 (6.16)
| 0.0013 | NS |
ETV7
| 171 |
4 (0.8)
| 0.088 |
14 (5.4)
| 0.5 |
35 (28.7)
| 1 |
14 (6.08)
| 0.0011 | NS |
-
Regulon size, the number of genes in the regulatory network for each TF; # hit, the number of genes, among each TF regulatory network that we annotate as a GWAS-linked gene (in parenthesis: expected number of GWAS genes in the regulatory network of the TF); FDR, false discovery rate of the overrepresentation of GWAS hits in the TF regulatory network (hypergeometric test; see the ‘Methods’ section). For the GWAS genes, each test is performed for 3 sets of genes defined using a hard (P < 1e−06; 44 genes); lenient (P < .05; 569 genes) or no threshold (3181 genes) on eQTL significance levels. For the ‘response genes’, only one test is performed with all the response genes