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Table 5 Comparison of scoring functions on p53 dataset

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

  GSZ iGA t-test modKS KS
1 *BP:0001836: release of cytochrome c from mitochondria* *BP:0001836: release of cytochrome c from mitochondria* CC:0009434: microtubule-based flagellum *BP:0001836: release of cytochrome c from mitochondria* BP:0050962: detection of light...
2 BP:0051668: localization within membrane CC:0031903: micro-body membrane MF:0033558: protein deacetylase activity BP:0050953: sensory perception of light stimulus BP:0050908: detection of light...
3 CC:0031903: micro-body membrane CC:0005778: peroxisomal membrane MF:0004407: histone deacetylase activity BP:0007601: visual perception BP:0007602: phototransduction
4 CC:0005778: peroxisomal membrane CC:0044438: micro-body part CC:0031903: micro-body membrane CC:0000118: histone deacetylase complex BP:0009584: detection of visible light
5 BP:0042787: protein ubiquitination... catabolic process CC:0044439: peroxisomal part CC:0005778: peroxisomal membrane MF:0001664: G-protein-coupled receptor binding BP:0009583: detection of light...
6 *BP:0008637: apoptotic mitochondrial changes* BP:0042787: protein ubiquitination... catabolic process CC:0019861: flagellum BP:0015674: ditri-valent inorganic cation transport MF:0016018: cyclosporin A binding
7 CC:0044438: micro-body part BP:0050953: sensory perception of light stimulus CC:0044438: micro-body part MF:0033558: protein deacetylase activity *MF:0005086: ARF guanyl-nucleotide...*
8 CC:0044439: peroxisomal part BP:0007601: visual perception CC:0044439: peroxisomal part MF:0004407: histone deacetylase activity *BP:0032012: regulation of ARF protein signal...*
9 CC:0009434: microtubule-based flagellum MF:0033558: protein deacetylase activity BP:0030890: positive regulation of B cell proliferation BP:0006816: calcium ion transport *BP:0032011: ARF protein signal transduction*
10 BP:0051205: protein insertion into membrane MF:0004407: histone deacetylase activity BP:0050962: detection of light... MF:0019237: centromeric DNA binding CC:0031903: micro-body membrane
11 BP:0046504: glycerol ether biosynthetic process CC:0009434: microtubule-based flagellum BP:0050908: detection of light... MF:0030170: pyridoxal phosphate binding CC:0005778: peroxisomal membrane
12 BP:0045017: glycerolipid biosynth... MF:0016018: cyclosporin A binding BP::0007602:: phototransduction BP:0008015: circulation MF:0033558: protein deacetylase activity
13 BP:0008643: carbohydrate transport MF:0019237: centromeric DNA... BP:0009584: detection of visible light BP:0035136: forelimb morphogenesis MF:0004407: histone deacetylase activity
14 *BP:0008629: induction of apoptosis by intracellular signals* BP:0051205: protein insertion into membrane CC:0000118: histone deacetylase complex BP:0015918: sterol transport CC:0031594: neuromuscular junction
15 *BP:0008635: caspase activation via cytochrome c* BP:0046504: glycerol ether biosynthetic process BP:0018298: protein-chromophore linkage BP:0030301: cholesterol transport MF:0005048: signal sequence binding
  1. Biological classes reported by each scoring function from p53 dataset. Apoptosis related classes are highlighted with asterisk before and after the class name. Clear apoptosis classes are shown with bold font and border cases with underlined font. Although many methods report same apoptosis GO class as the top class, only GSZ is able to report three other apoptosis GO classes. Furthermore, our supplementary table S1 [see additional file 7] shows that GSZ reports strongest p-values for reported apoptosis gene sets.