Table 3.
GWAS Data Pathways Significantly Associated with Consortium Lung Phenotype
|
ID |
Name |
Genes (n) |
Corrected p Valuea |
Z Score |
Genes with Gene-Level p Value < 0.05 (Ordered by p Value) |
|---|---|---|---|---|---|
| Analyses Included All Available Pathwaysb | |||||
| KEGG Pathways | |||||
| 05320 | autoimmune thyroid disease | 49 | 0.002 | 4.469 | HLA-DRB1; HLA-DQA1; HLA-DRA; IFNA13; IFNA8; IFNA2; IFNA16; IFNA17; IFNA6; IFNA10; IFNA1; IFNA7; IFNA14; IFNA4; HLA-DQB1; IFNA5; IFNA21; HLA-E; HLA-DQA2 |
| 04672 | intestinal immune network for IgA production | 45 | 0.018 | 3.822 | HLA-DRB1; HLA-DQA1; HLA-DRA; TNFRSF17; HLA-DQB1; CXCL12; HLA-DQA2 |
| MSigDB Pathways | |||||
| TGCAAAC.MIR-452 | 106 | 0.049 | 3.676 | SAV1; TRPS1; ATL1; ZIC1; NIN; SH3BGRL; SYN3; XPNPEP1; XPO4; RAB8B | |
| Analyses Confined to Pathways Significant for Differential Expressionc | |||||
| GO Cellular Component Pathways | |||||
| 0030134 | ER to Golgi transport vesicle | 39 | 0.001 | 4.271 | HLA-DRB1; HLA-DQA1; HLA-DRA; MCFD2; HLA-DQB1; SEC24B; HLA-E; SREBF1; HLA-DQA2 |
| 0012507 | ER to Golgi transport vesicle membrane | 33 | 0.001 | 4.218 | HLA-DRB1; HLA-DQA1; HLA-DRA; MCFD2; HLA-DQB1; SEC24B; HLA-E; SREBF1; HLA-DQA2 |
| CF Relevant Custom Pathways | |||||
| ER stress response | 248 | 0.029 | 1.962 | FGFR4; HMOX1; UBE2L6; TAX1BP1; CREB3; ARL1; UBXN4; RNF5; ATF6B; USO1; GADD45A; NIPSNAP1; XBP1; AMFR; TOR1A; SREBF1; PSMB2 | |
| HLA-Specific Pathways | |||||
| class I | 7 | 0.0382 | 1.842 | HLA-E | |
| class II | 11 | 0.0254 | 2.285 | HLA-DRB1; HLA-DQA1; HLA-DRA; HLA-DQB1; HLA-DQA2 | |
| class I and class II | 18 | 0.0101 | 2.771 | HLA-DRB1; HLA-DQA1; HLA-DRA; HLA-DQB1; HLA-E; HLA-DQA2 | |
Default parameters with 1,000 resamples were used, and pathways were limited to those that contained ≥10 but ≤200 genes. GeneSetScan utilizes a mapping of SNPs to genes based upon a reference panel from HapMap release 23a and mapped genes to pathways based upon a March 2011 release of GO and KEGG pathways. The number of permutations for the HLA-specific analysis was increased to 10,000 to improve precision for this relevant group of genes. See Table S6 (tab B) for the inclusive list of genes for these pathways. See Table S5 for gene MIM numbers.
Multiple comparison corrected p.
Gene level p values calculated using family-wise (all SNPs, genes, and pathways tested) as provided by GeneSetScan.
Pathways listed in Table 2 were evaluated for association to genotype. Pathways are listed in this table if p value < 0.05.