Project: vulpe_liver_2014
120 significantly associated models · 34 unique genes
| # | chr | p0 | p1 | # assoc genes | # joint models | best TWAS P | best SNP P | cond SNP P | % var exp | joint genes |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1 | 201865024 | 202832586 | 1 | 1 | 7.1e-11 | 4.1e-02 | 0.002 | -127 | Ccs |
| 2 | 1 | 231783442 | 237140824 | 27 | 1 | 1.2e-09 | 1.0e-08 | 0.382 | 98 | Marchf5 |
| 3 | 1 | 238391248 | 240123287 | 5 | 1 | 9.1e-08 | 1.0e-07 | 1.000 | 100 | Sorbs1 |
| 4 | 14 | 34177603 | 35456143 | 1 | 1 | 3.0e-07 | 2.2e-03 | 1.000 | 100 | Ociad2 |
p0: physical position of the start of the locus. p1: physical position of the end of the locus. # joint models: number of models selected by step-wise conditional analysis.
| Trait | chisq ratio | # genes+ | # genes++ | % genes++ | corr | corr P | genes |
|---|---|---|---|---|---|---|---|
| Food consumed during 24 hour testing period | 18.6 | 1 | 0 | 0 | 0.00 | 1.0e+00 | Ccs |
| Water consumed over 24 hour session | 11.5 | 1 | 0 | 0 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_spc9 | 12.9 | 1 | 0 | 0 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_spc8 | 48.6 | 1 | 1 | 25 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_mpc4 | 43.2 | 1 | 1 | 25 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_spc4 | 9.9 | 1 | 0 | 0 | 0.00 | 1.0e+00 | Cyp26a1 |
| tautz: manual_spc10 | 28.4 | 1 | 1 | 25 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_spc23 | 8.8 | 4 | 0 | 0 | 1.00 | 1.1e-04 | Fra10ac1 Myof Cyp26a1 Ffar4 |
| tautz: manual_mpc2 | 16.6 | 1 | 0 | 0 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_spc1 | 24.0 | 1 | 1 | 25 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_spc16 | 19.8 | 1 | 0 | 0 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_spc5 | 8.9 | 1 | 0 | 0 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_spc3 | 10.5 | 1 | 0 | 0 | 0.00 | 1.0e+00 | Tnks2 |
| tautz: manual_mpc11 | 24.9 | 1 | 1 | 25 | 0.00 | 1.0e+00 | Ccs |
| tautz: manual_mpc1 | 37.0 | 1 | 1 | 25 | 0.00 | 1.0e+00 | Ccs |
| Liver iron concentration | 23.9 | 1 | 1 | 25 | 0.00 | 1.0e+00 | Ccs |
| Liver cobalt concentration | 35.3 | 1 | 1 | 25 | 0.00 | 1.0e+00 | Ccs |
| Liver zinc concentration | 13.7 | 7 | 1 | 25 | 0.98 | 3.9e-10 | Marchf5 Ppp1r3c Rpp30 Cpeb3 Ccs Tnks2 NA |
chisq ratio: Average Chi2 statistic for the selected genes in the secondary trait, divided by the average statistic for all genes in the secondary trait. # genes+: Shared significant genes at Bonferroni correction. # genes++: Shared significant genes at transcriptome-wide significance. % genes++: Number of [++] genes as a percentage of primary trait’s total joint genes. corr: Correlation of effect sizes across the [+] genes.
| tissue | modality | # hits | % hits/tests | avg chisq |
|---|---|---|---|---|
| Adipose | alternative polyA | 0 | 0.000 | 1.06 |
| Adipose | alternative TSS | 0 | 0.000 | 1.16 |
| Adipose | gene expression | 5 | 0.060 | 1.18 |
| Adipose | isoform ratio | 0 | 0.000 | 1.14 |
| Adipose | intron excision ratio | 8 | 0.274 | 1.39 |
| Adipose | mRNA stability | 4 | 0.116 | 1.21 |
| BLA | alternative polyA | 0 | 0.000 | 1.16 |
| BLA | alternative TSS | 0 | 0.000 | 1.08 |
| BLA | gene expression | 4 | 0.066 | 1.19 |
| BLA | isoform ratio | 1 | 0.057 | 1.18 |
| BLA | intron excision ratio | 0 | 0.000 | 1.29 |
| BLA | mRNA stability | 1 | 0.049 | 1.18 |
| Brain | alternative polyA | 0 | 0.000 | 1.15 |
| Brain | alternative TSS | 4 | 0.233 | 1.34 |
| Brain | gene expression | 8 | 0.088 | 1.20 |
| Brain | isoform ratio | 3 | 0.095 | 1.17 |
| Brain | intron excision ratio | 9 | 0.166 | 1.32 |
| Brain | mRNA stability | 3 | 0.069 | 1.17 |
| Eye | alternative polyA | 0 | 0.000 | 1.01 |
| Eye | alternative TSS | 0 | 0.000 | 1.21 |
| Eye | gene expression | 1 | 0.089 | 1.30 |
| Eye | isoform ratio | 0 | 0.000 | 1.09 |
| Eye | intron excision ratio | 1 | 0.163 | 1.29 |
| Eye | mRNA stability | 1 | 0.429 | 1.36 |
| IL | alternative polyA | 0 | 0.000 | 1.13 |
| IL | alternative TSS | 0 | 0.000 | 1.24 |
| IL | gene expression | 4 | 0.110 | 1.22 |
| IL | isoform ratio | 1 | 0.126 | 1.33 |
| IL | intron excision ratio | 1 | 0.103 | 1.26 |
| IL | mRNA stability | 0 | 0.000 | 1.10 |
| LHb | alternative polyA | 0 | 0.000 | 1.02 |
| LHb | alternative TSS | 0 | 0.000 | 1.13 |
| LHb | gene expression | 6 | 0.187 | 1.24 |
| LHb | isoform ratio | 0 | 0.000 | 1.11 |
| LHb | intron excision ratio | 1 | 0.097 | 1.38 |
| LHb | mRNA stability | 1 | 0.097 | 1.18 |
| Liver | alternative polyA | 2 | 0.133 | 1.16 |
| Liver | alternative TSS | 0 | 0.000 | 1.31 |
| Liver | gene expression | 5 | 0.070 | 1.20 |
| Liver | isoform ratio | 2 | 0.084 | 1.26 |
| Liver | intron excision ratio | 1 | 0.023 | 1.27 |
| Liver | mRNA stability | 2 | 0.081 | 1.25 |
| NAcc | alternative polyA | 0 | 0.000 | 1.22 |
| NAcc | alternative TSS | 4 | 1.166 | 1.29 |
| NAcc | gene expression | 4 | 0.122 | 1.23 |
| NAcc | isoform ratio | 1 | 0.135 | 1.19 |
| NAcc | intron excision ratio | 0 | 0.000 | 1.32 |
| NAcc | mRNA stability | 0 | 0.000 | 1.21 |
| NAcc2 | alternative polyA | 0 | 0.000 | 1.10 |
| NAcc2 | alternative TSS | 1 | 0.136 | 1.12 |
| NAcc2 | gene expression | 5 | 0.094 | 1.22 |
| NAcc2 | isoform ratio | 0 | 0.000 | 1.11 |
| NAcc2 | intron excision ratio | 3 | 0.113 | 1.32 |
| NAcc2 | mRNA stability | 3 | 0.168 | 1.22 |
| OFC | alternative polyA | 0 | 0.000 | 1.17 |
| OFC | alternative TSS | 0 | 0.000 | 0.93 |
| OFC | gene expression | 5 | 0.135 | 1.19 |
| OFC | isoform ratio | 0 | 0.000 | 1.20 |
| OFC | intron excision ratio | 0 | 0.000 | 1.33 |
| OFC | mRNA stability | 0 | 0.000 | 1.13 |
| PL | alternative polyA | 0 | 0.000 | 1.19 |
| PL | alternative TSS | 0 | 0.000 | 1.18 |
| PL | gene expression | 5 | 0.134 | 1.21 |
| PL | isoform ratio | 0 | 0.000 | 1.06 |
| PL | intron excision ratio | 0 | 0.000 | 1.28 |
| PL | mRNA stability | 0 | 0.000 | 1.11 |
| PL2 | alternative polyA | 0 | 0.000 | 1.17 |
| PL2 | alternative TSS | 1 | 0.106 | 1.17 |
| PL2 | gene expression | 5 | 0.078 | 1.17 |
| PL2 | isoform ratio | 1 | 0.054 | 1.17 |
| PL2 | intron excision ratio | 1 | 0.032 | 1.32 |
| PL2 | mRNA stability | 2 | 0.082 | 1.21 |
avg chisq: Average Chi2 (squared Z-score) across all models in this panel for this trait.