Table 1 General information on the tested pathway activity inference methods
From: Robustness evaluations of pathway activity inference methods on gene expression data
Method | Description | Category | Pathway representation | References |
|---|---|---|---|---|
COMBINER | Multi-level optimisation framework for core module inference | Non-TB | GS | [31] |
PAC | Pathway activity inference scheme in a condition-specific manner | Non-TB | GS | [16] |
PLAGE | Pathway level analysis of gene expression based on singular value decomposition (SVD) | Non-TB | GS | [32] |
GSVA | Gene set enrichment based on Kolmogorov Smirnov-like random statistic | Non-TB | GS | [33] |
DRW | Random walk restart on KEGG network | PTB | PT | [13] |
sDRW | Random walk restart on KEGG network | PTB | PT | [34] |
e-DRW | Bi-random walk restart on KEGG and NCI-PID network separately | PTB | PT | [35] |