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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.