Table 3.
Top 20 canonical pathways for QTL identified for all traits, and for co-localized QTL
| Pathways for all identified QTL | |||
|---|---|---|---|
| Pathway | P-value | Ratio: | Genes in pathway that were identified in current study |
| 1D-myo-inositol Hexakisphosphate Biosynthesis II (Mammalian) | 1.93E-03 | 4/19 | INPP5E,IPMK,SEC16A,PMPCA |
| AMPK Signaling | 2.15E-03 | 13/178 | CHRNA5,MTOR,STRADA,AK8,INSR,CHRNA3,PPM1J,CHRNB4,PIK3R2,ADRA2A,TSC1,FOXO1,ADRA1A |
| Angiopoietin Signaling | 1.22E-03 | 6/66 | NRAS,PIK3R2,BIRC5,CASP9,IKBKAP,FOXO1 |
| Calcium Signaling | 1.51E-02 | 11/178 | CALR,CHRNA5,MYL4,CHRNB4,CAMK4,CHRNA3,CAMK1G,MEF2D,TPM1,RAP1A,MEF2A |
| Cardiac Hypertrophy Signaling | 5.80E-03 | 14/223 | MTOR,MYL4,CAMK4,RHOC,IGF1R,NRAS,PIK3R2,RHOT1,ADRA2A,MEF2D,MAP3K3,CACNA1D,MEF2A,ADRA1A |
| D-myo-inositol (1,3,4)-trisphosphate Biosynthesis | 1.93E-03 | 4/19 | INPP5E,IPMK,SEC16A,PMPCA |
| D-myo-inositol (1,4,5)-trisphosphate Degradation | 1.44E-02 | 3/18 | INPP5E,SEC16A,PMPCA |
| Dopamine Degradation | 8.29E-03 | 4/28 | ALDH1A1,ALDH1A3,MAOB,ALDH4A1 |
| ERK5 Signaling | 2.28E-03 | 7/63 | MAP2K5,NRAS,NTRK1,MEF2D,NGF,MAP3K3,MEF2A |
| Ethanol Degradation IV | 4.02E-03 | 4/23 | ALDH1A1,TYRP1,ALDH1A3,ALDH4A1 |
| Glioblastoma Multiforme Signaling | 1.03E-02 | 10/146 | WNT2B,IGF1R,NRAS,MTOR,PIK3R2,WNT5A,RHOC,RHOT1,TSC1, FOXO1 |
| Glioma Signaling | 7.71E-03 | 8/98 | ABL1,TGFA,IGF1R,NRAS,MTOR,PIK3R2,CAMK4,CAMK1G |
| Histamine Degradation | 1.22E-02 | 3/17 | ALDH1A1,ALDH1A3,ALDH4A1 |
| Human Embryonic Stem Cell Pluripotency | 1.85E-03 | 11/134 | WNT2B,PIK3R2,WNT5A,SMAD3,SMAD6,NTRK1,TCF7L2,BMP2,NGF,FOXO1,NOG |
| Non-Small Cell Lung Cancer Signaling | 1.13E-02 | 6/65 | ABL1,TGFA,NRAS,PIK3R2,CASP9,RXRA |
| Nur77 Signaling in T Lymphocytes | 1.26E-03 | 7/57 | MAP2K5,SIN3B,CASP9,RXRA,CAMK4,MEF2D,MAP3K3 |
| Putrescine Degradation III | 2.84E-03 | 4/21 | ALDH1A1,ALDH1A3,MAOB,ALDH4A1 |
| Superpathway of D-myo-inositol (1,4,5)-trisphosphate Metabolism | 4.71E-03 | 4/24 | INPP5E,IPMK,SEC16A,PMPCA |
| Thyroid Cancer Signaling | 9.69E-04 | 6/40 | NRAS,RET,RXRA,NTRK1,TCF7L2,NGF |
| Tryptophan Degradation X (Mammalian, via Tryptamine) | 4.02E-03 | 4/23 | ALDH1A1,ALDH1A3,MAOB,ALDH4A1 |
| Pathways identified for co-localized QTL | |||
| Pathway | P-value | Ratio: | Genes in pathway that were identified in current study |
| 2-oxobutanoate Degradation I | 4.22E-02 | 1/5 | MCEE |
| AMPK Signaling | 4.42E-03 | 6/178 | CHRNA5,PPM1J,CHRNB4,INSR,CHRNA3,ADRA1A |
| Calcium Signaling | 1.55E-04 | 8/178 | CALR,CHRNA5,CHRNB4,CHRNA3,CAMK1G,TPM1,RAP1A,MEF2A |
| Cardiac Hypertrophy Signaling | 4.35E-02 | 5/223 | IGF1R,NRAS,RHOC,MEF2A,ADRA1A |
| CDK5 Signaling | 4.94E-02 | 3/105 | NRAS,PPM1J,NGF |
| Cholecystokinin/Gastrin-mediated Signaling | 4.95E-02 | 3/245 | NRAS,RHOC,MEF2A |
| CTLA4 Signaling in Cytotoxic T Lymphocytes | 4.01E-02 | 3/88 | PPM1J,PTPN22,AP1M1 |
| ERK5 Signaling | 1.69E-02 | 3/63 | NRAS,NGF,MEF2A |
| Germ Cell-Sertoli Cell Junction Signaling | 4.93E-02 | 4/160 | NRAS,TJP1,RHOC,RAB8B |
| Glioblastoma Multiforme Signaling | 3.73E-02 | 4/146 | WNT2B,IGF1R,NRAS,RHOC |
| Glioma Signaling | 1.01E-02 | 4/98 | TGFA,IGF1R,NRAS,CAMK1G |
| Integrin Signaling | 3.33E-02 | 5/207 | NRAS,TSPAN2,RHOC,TLN2,RAP1A |
| Methylmalonyl Pathway | 3.39E-02 | 1/4 | MCEE |
| mTOR Signaling | 2.28E-02 | 5/187 | NRAS,PPM1J,INSR,RHOC,RPS15 |
| NF-κB Signaling | 1.65E-02 | 5/172 | TGFA,IGF1R,NRAS,INSR,NGF |
| PTEN Signaling | 1.89E-02 | 4/118 | IGF1R,NRAS,INSR,MAGI3 |
| Renal Cell Carcinoma Signaling | 2.32E-02 | 3/71 | TGFA,NRAS,RAP1A |
| STAT3 Pathway | 2.49E-02 | 3/73 | IGF1R,NRAS,INSR |
| TCA Cycle II (Eukaryotic) | 1.65E-02 | 2/23 | IDH3A,ACO1 |
| Thyroid Cancer Signaling | 4.62E-02 | 2/40 | NRAS,NGF |
All characterized genes within significant QTL regions were used as input in Ingenuity Pathway Analysis (IPA) software. The Top 20 significant (P ≤ 0.05) pathways are listed. The results are displayed for pathways identified when using all QTL regions (61 total QTL) which resulted in 682 (999 total) annotated genes used for pathway analysis. The bottom section of the table displays the pathways identified when using only the co-localized QTL regions (7 total co-localized QTL regions) which resulted in 185 (226 total) annotated genes used for pathway analysis. The pathways are the top canonical pathways identified by IPA and are listed in alphabetical order. The ratio refers to the number of genes that were identified in the current study compared to the total number of genes that are in the pathway according to IPA