Table 1.
Principal component variance analysis (PCVA) decomposition of sources of variance
| Gene expression | PSI (108,091 exon bins) |
PSI (7001 exon bins) |
|
|---|---|---|---|
| Principal component | |||
| PC1 | 28.9% | 7.6% | 9.3% |
| PC2 | 25.1% | 5.5% | 6.9% |
| PC3 | 5.2% | 4.1% | 4.1% |
| PC4 | 4.4% | 3.0% | 3.2% |
| PC5 | 3.5% | 2.6% | 2.9% |
| PC6 | 2.3% | 2.4% | 2.7% |
| PC7 | 2.0% | 2.3% | 2.3% |
| PC8 | 1.6% | 1.8% | 2.0% |
| PC9 | 1.6% | 1.7% | 1.9% |
| PC10 | 1.3% | 1.7% | 1.6% |
| SUM of PC1–PC10 | 75.9% | 33.0% | 27.9% |
| Variance component | |||
| Ancestry | 2.3% | 5.8% | 5.3% |
| Location | 0.2% | 0.7% | 0.5% |
| Disease | 40.3% | 20.7% | 27.9% |
| Location*disease | 0.8% | 0.8% | 1.0% |
The table shows the percent variance in gene expression or splicing (PSI at two inclusion thresholds) explained by the first ten PCs and their sum, as well as the weighted contribution of each variance component term (ancestry, disease, location, and the interaction of disease and location) to these 10 PCs. Gene expression is for 18,929 genes, and number of PSI bins is before and after the final two stages of filtering (n = 119 samples for all)