Table 3.
IPA summary of associated networks, molecular and cellular functions, diseases and disorders and canonical pathways for the 38 genes mapped to private SNPs.
| IPA categories | Statistical measures | Associated gene(s) |
|---|---|---|
| Associated network functions | Network score * | |
| Immune and lymphatic system development and function, cardiovascular system development and function, cell death |
25 |
AR, CDH2, CNTN4, DOK5, EDA2R, FREQ, GRMB, IFNG,
MYRIP, NEUROG3, VSIG4 |
| Cancer, cellular growth and proliferation, reproductive system disease |
25 |
ABCB7, CACNA18, DSCAM, EXOC6B, HEPH, IER5L,
NPNT, PRDM5, PSCD3, SDK1, XPA |
| Cellular assembly and organization, nervous system development and function, cell morphology |
7 | ARHGAP6, ARHGEF9, DLC1, PAK3 |
| Molecular and cellular functions | p-value ‡ | |
| Cell–cell signaling and interaction | 1.87E-04–1.16E-02 |
AR, CDH2, IFNG, CACNA1B, FREQ, GRM8, CNTN4,
DSCAM, NPNT, PSCD3 |
| Cellular assembly and organization | 2.63E-04–1.16E-02 | ARHGEF9, CDH2, IFNG, PAK3, AR, XPA, CDH2 |
| Cell death | 6.18E-04–1.16E-02 | CDH2, IFNG, PRDM5, AR |
| Gene expression | 8.77E-04–1.16E-02 | AR, IFNG, XPA, USP11, |
| Cellular compromise | 1.07E-03–1.16E-02 | AR, IFNG, USP11, XPA, CDH2, SDK1, ARHGAP24 |
| Associated disease and disorders | p-value ‡ | |
| Nutritional disease | 4.70E-04–4.70E-04 | AR, XPA |
| Reproductive system disease | 6.18E-04–1.16E-02 | CDH2, IFNG, PRDM5, AR, DLC1 |
| Immunological disease | 7.14E-04–9.31E-03 | AR, IFNG, XPA |
| Hematological disease | 1.41E-03–9.31E-03 | IFNG, XPA, ABCB7, AR |
| Cancer | 2.34E-03–1.16E-02 | IFNG, PRDM5, PAK3, AR, CDH2, DLC1, NPNT, XPA |
| Top canonical pathways | p-value ‡ | |
| Interferon signaling | 6.57E-02 | IFNG |
| Protein ubiquitination pathway | 6.7E-02 | IGNG, USP11 |
| Leukocyte extravasation signaling | 6.96E-02 | ARHGAP6, DLC1 |
| Nucleotide excision repair pathway | 7.66E-02 | XPA |
| Glucocorticoid receptor signaling | 1.14E-01 | AR, IFNG, |
| Physiological system development and function | p-value ‡ | |
| Skeletal and muscular system development and function |
1.87E-04–1.16E-02 | AR, CDH2, IFNG |
| Tissue morphology | 1.07E-03–1.16E-02 | CDH2, IFNG, NEUROG3, AR |
| Cardiovascular system development and function | 2.34E-03–1.16E-02 | CACNA1B, ARHGAP24, CDH2, IFNG |
| Connective tissue development and function | 2.34E-03–1.16E-02 | IFNG, AR, ARHGAP24, |
| Hair and skin development and function | 2.34E-03–1.16E-02 | CDH2, IFNG |
| Digestive system development and function | 2.34E-03–2.34E-03 | IFNG |
*
Networks with scores ≥3 have a 99.9% confidence of not being generated by random chance.
‡
The IPA computes p-values of statistically significant findings by comparing the number of molecules of interest relative to the total number of occurrences of these molecules in all functional/pathway annotations stored in the Pathways Knowledge Base (Fisher’s exact test with p-value adjusted using the Benjamini–Hochberg multiple testing correction).
IPA: Ingenuity Pathways Analysis.