TABLE 6.
Ingenuity pathway analysis summary
| Functional analysis of networka | ||
|---|---|---|
| No. of molecules | P value | |
| Diseases and disorders | ||
| Cancer | 125 | 3.21 × 10–3 – 9.40 × 10–14 |
| Organismal injury and abnormalities | 77 | 2.75 × 10–3 – 6.44 × 10–9 |
| Reproductive system disease | 60 | 2.65 × 10–3 – 6.44 × 10–9 |
| Molecular and cellular functions | ||
| Cellular development | 75 | 2.93 × 10–3 – 8.45 × 10–9 |
| Cellular growth and proliferation | 78 | 2.93 × 10–3 – 8.45 × 10–9 |
| Cellular movement | 58 | 3.21 × 10–3 – 1.07 × 10–8 |
| Physiological systems | ||
| Skeletal and muscular system development and function | 28 | 2.31 × 10–3 – 8.45 × 10–9 |
| Tumor morphology | 40 | 2.68 × 10–3 – 1.27 × 10–7 |
| Cardiovascular system development and function | 49 | 2.93 × 10–3 – 3.63 × 10–7 |
| Canonical pathway analysisb | ||
|---|---|---|
| Top canonical pathways | Ratio | P valued |
| Hepatic fibrosis/hepatic stellate cell activation | 11/155 | 4.73 × 10–7 |
| HMGB1 signaling | 8/109 | 9.83 × 10–6 |
| Regulation of cellular mechanics by calpain protease | 6/73 | 6/73 3.78 × 10–5 |
| Upstream regulator analysisc | ||
|---|---|---|
| Top transcription factors | Predicted activation state | P value of overlap |
| F2 | Activated | 7.77 × 10–13 |
| HGF | Activated | 6.25 × 10–10 |
| VEGF | Activated | 9.72 × 10–10 |
HGF, hepatocyte growth factor; HMGB1, high mobility group box-1; VEGF, vascular endothelial growth factor.
Identified biological functions and/or diseases that were overrepresented among molecules in network using right-tailed Fisher exact test
Identified pathways from Ingenuity Pathway Analysis library that were most significant to data set. Significance of association was measured in 2 ways: (1) as ratio of number of molecules from focus gene set that map to pathway to total number of molecules that map to canonical pathway; and (2) using Fisher exact test
Based on prior knowledge of expected effects between transcription factors and their target genes stored in Ingenuity Pathway Analysis library. Overlap P value measures whether there is statistically significant overlap between data set genes and genes regulated by transcription factor using Fisher exact test
Range of P values indicates that category listed in table contained several subcategories. P values provide range from least to most significant for all subcategories.