Table 3. Specific pathways for HAM/TSP.
| Pathway ID of TRANSPATHa database | Pathway nameb | Group sizec | Number of hits in groupd | Number of hits expectede | P-valuef |
|---|---|---|---|---|---|
| CH000003804 | ABL → TOPBP1 | 3 | 2 | 1 | 0.00021 |
| CH000000870 | ABL → Rad52 | 4 | 2 | 1 | 0.00043 |
| CH000000972 | ABL—/ Bcl-xL | 4 | 2 | 1 | 0.00043 |
| CH000003546 | ABL → Caspase-9 | 4 | 2 | 1 | 0.00043 |
| CH000000867 | ABL → p73α | 5 | 2 | 1 | 0.00071 |
| CH000000908 | Caspase-8 → ABL | 6 | 2 | 1 | 0.0011 |
| CH000000997 | Ubc9 —/ p73α | 7 | 2 | 1 | 0.0015 |
| CH000000895 | Fas → ABL | 10 | 2 | 1 | 0.0031 |
| CH000000977 | ABL → p53 | 11 | 2 | 1 | 0.0038 |
| CH000000869 | p73 pathway | 24 | 2 | 1 | 0.018 |
| CH000000711 | TGFβ pathway | 76 | 3 | 1 | 0.026 |
| CH000000879 | Caspase network | 93 | 3 | 1 | 0.044 |
a: TRANSPATH is a manually curated database of signal transduction pathways.
b: Pathway name and genes are described as in TRANSPATH. ABL: c-abl oncogene 1, non-receptor tyrosine kinase; TOPBP1: DNA topoisomerase II binding protein 1; RAD52: RAD52 (S. cerevisiae) homolog, DNA repair protein; TP73: tumor protein p73 isoform ɑ; Ubc9: UBE21 (ubiquitin-conjugating enzyme E2I). Symbols in pathway name represent type of reaction (e.g. →: facilitation; —/: inhibition).
c: Group size: the total number of genes, proteins, and metabolites which exist within the pathway of interest.
d: Number of hits in group: number of the cellular genes of interest (e.g. up-regulated DEGs only in HAM/TSP), which exist within the pathway chosen by a statistical test.
e: Number of hits expected: number of the cellular genes of interest that are included in the pathway chosen by statistical test by chance.
f. P-value of two-tailed Fisher’s exact test.