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Table 6 Comparison of GSZ and program packages using p53 dataset

From: Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function

  GSZ-score GSA SP GSEA
1 *BP:0001836: release of cytochrome c from mitochondria* CC:0031903: micro-body membrane CC:0009434: microtubule-based flagellum CC:0000118: histone deacetylase complex
2 BP:0051668: localization within membrane CC:0005778: peroxisomal membrane MF:0005125: cytokine activity BP:0009314: response to radiation
3 CC:0031903: micro-body membrane CC:0009434: microtubule-based flagellum CC:0019861: flagellum BP:0050962: detection of light...
4 CC:0005778: peroxisomal membrane CC:0044438: micro-body part BP:0050962: detection of light... BP:0050908: detection of light...
5 BP:0042787: protein ubiquitination... CC:0044439: peroxisomal part BP:0050908: detection of light... BP: 0007602: phototransduction
6 *BP:0008637: apoptotic mitochondrial changes* *BP:0001836: release of cytochrome c from mitochondria* BP:0007602: phototransduction BP:0009584: detection of visible light
7 CC:0044438: micro-body part CC:0005626: insoluble Fraction BP: 0009584: detection of visible light BP:0009583: detection of light...
8 CC:0044439: peroxisomal part CC:0019861: flagellum *BP:0001836: release of cytochrome c from mitochondria* MF:0030170: pyridoxal phosphate binding
9 CC:0009434: microtubule-based flagellum MF:0015103: inorganic anion transmembrane... BP:0009583: detection of light... *BP:0001836: release of cytochrome c from mitochondria*
10 BP:0051205: protein insertion into mem brane BP:0051668: localization within membrane BP:0006955: immune response MF:0005487: nucleocytoplasmic trans porter activity
11 BP:0046504: glycerol ether biosynthetic process BP:0050962: detection of light... BP:0030890: positive regulation of B cell proliferation BP:0006654: phosphatidic acid biosynthetic process
12 BP:0045017: glycerolipid biosynthetic process BP:0050908: detection of light... MF:0001664: G-protein-coupled receptor binding BP:0046473: phosphatidic acid metabolic process
13 BP:0008643: carbohydrate transport BP:0007602: photo-transduction BP:0006572: tyrosine catabolic process BP:0035137: hindlimb morphogenesis
14 *BP:0008629: induction of apoptosis by intracellular signals* BP:0009584: detection of visible light MF:0008009: chemokine activity BP:0051716: cellular response to stimulus
15 *BP:0008635: caspase activation via cytochrome c* CC:0031594: neuromuscular junction MF:0042379: chemokine receptor binding BP:0008217: blood pressure regulation
  1. Table compares GSZ analysis with three popular software packages. Apoptosis related positive classes are highlighted as in table 5. GSZ, GSA and SP reported classes with strong signal, whereas GSEA did not report any significant classes. GSZ, GSA and SP reported strong p-value for GO class 1836, but only GSZ ranks it as top class. GSZ also reports 3 other apoptosis related classes.