Rank | Hypothesis Name | Correct | Incorrect | Score | Ternary Dot Product p | Causal Graph p |
|---|
1 | Response to Hypoxia+ | 48 | 9 | 37 | 2 × 10-12 | < 0.001 |
2 | Dexamethasone+ | 20 | 4 | 16 | 6 × 10-6 | < 0.001 |
3 | Hydrocortisone+ | 17 | 4 | 13 | 1 × 10-8 | < 0.001 |
4 | PGR+ | 12 | 1 | 11 | 6 × 10-8 | < 0.001 |
5 | SRF+ | 10 | 0 | 10 | 3 × 10-5 | < 0.001 |
6 | KLF4+ | 9 | 0 | 9 | 3 × 10-6 | < 0.001 |
7 | NR3C1+ | 12 | 4 | 8 | 7 × 10-4 | < 0.001 |
7 | Glucocorticoid+ | 12 | 4 | 8 | 8 × 10-5 | < 0.001 |
7 | CCND1+ | 9 | 1 | 8 | 3 × 10-4 | < 0.001 |
7 | Triamcinolone acetonide+ | 8 | 0 | 8 | 9 × 10-7 | < 0.001 |
... | ... | ... | ... | ... | ... | ... |
17 | NRF2+ | 9 | 4 | 5 | 0.18 | 0.07 |
- Top hypotheses by score in an example experimental dataset of dexamethasone-stimulated chondrocytes (GEO accession GSE7683 [21]). Each hypothesis is scored by the difference between the numbers of correct and incorrect predictions. Significance is assessed by the Ternary Dot Product and Causal Graph Randomization p-values discussed in the text; the latter numbers are estimates based on 1000 runs of graph randomization and for this reason are always a multiple of 0.001. When no randomized graph with a better score for the given hypothesis is detected, we indicate that as "p < 0.001." Note that hypotheses with the same numbers of correct and incorrect predictions do not necessarily have the same p-values because the significance calculation takes into account the full contingency table for each hypothesis; some hypotheses result in more predicted regulations than others.
