Table 8

A specificity analysis of the target pathways on 16 cancer data sets
Pathway type Statistic GSEA GSA PADOG
Target p med 0.2603 0.087 0.043
Target rank med 39.56 10.15 6.42
Apoptosis p med 0.3329 0.203 0.1985
Apoptosis rank med 37.56 24.24 28.76
Cell cycle p med 0.3133 0.325 0.227
Cell cycle rank med 26.29 36.35 28.61
Pathways in cancer p med 0.351 0.114 0.0465
Pathways in cancer rank med 47.54 13.21 8.41
RNA polymerase p med 0.5 0.681 0.6485
RNA polymerase rank med 57.78 71.51 63.33

The table shows a comparison between the pathways specifically designed by KEGG for each type of cancer (Target pathways) and other pathways that are commonly involved in many cancers. The table shows statistics computed from nominal p-values, and ranks of each type of pathway for the 16 cancer datasets shown in Table 1. PADOG gives the most significant p-values and best ranks to the target pathways. For each analysis method, the values for type of pathway with the smallest median p-values and ranks (strongest association with the phenotype) are shown in bold, while the second smallest values are italicized.

Tarca et al.

Tarca et al. BMC Bioinformatics 2012 13:136   doi:10.1186/1471-2105-13-136

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