Table 2.
Overview of self-contained gene set and pathway methods
| Principle Method | Reference | Software |
|---|---|---|
| Average of single-gene statistics |
[79] |
sigPathway |
| Linear Model Toolset for GSEA |
[80] |
GSEAlm |
| SAM-GS |
[81] |
|
| Globaltest |
[82] |
globaltest |
| GlobalANCOVA |
[83] |
GlobalAncova |
| Hotelling’s T2 |
[84-87] |
PCOT2 |
| N-statistic |
[88] |
cramer |
| RCMAT |
[89] |
|
| Non-linear tests for identifying differentially expressed genes or genetic networks |
[87] |
|
| Pathway-express |
[90] |
|
| Signaling Pathway Impact Analysis |
[91] |
SPIA (Bioconductor) |
| SEPEA |
[92] |
|
| PARADIGM |
[93] |
|
| Gene set analysis exploiting the topology of a pathway | [94] | IPS (available upon request) |