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Table 4 Top 20 significant HYPs for TNF data set (GSE2638)

From: Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data

Mechanism Direction Correct Richness Concordance Ambiguous Contra Possible Observed
tscript(complex(NCH:“Nfkb Complex”)) 1 69 6.2E-25 9.2E-16 2 5 417 76
path(SDIS:“bacterial infection”) 1 34 1.6E-10 1.0E-09 0 1 211 35
bp(GO:“replicative cell aging”) 1 33 3.1E-19 1.1E-07 0 3 121 36
p(PFH:“IFNA Family”) 1 25 4.0E-12 4.0E-07 0 1 105 26
a(CHEBI:lipopolysaccharide) 1 26 1.8E-06 7.6E-06 0 3 225 29
tscript(complex(NCH:“AP-1 Complex”)) 1 19 2.1E-04 2.0E-05 0 1 167 20
path(SDIS:“tissue damage”) 1 19 1.2E-03 2.0E-05 0 1 191 20
a(SCHEM:“Dietary Lipid”) 1 14 1.0E-07 6.1E-05 0 0 51 14
a(SCHEM:Allergens) 1 17 4.5E-08 7.2E-05 0 1 80 18
bp(GO:angiogenesis) 1 20 6.7E-09 2.4E-04 0 3 115 23
p(HGNC:AGT) 1 17 4.0E-06 3.6E-04 0 2 117 19
tscript(p(HGNC:TP63)) 1 17 1.2E-05 3.6E-04 0 2 126 19
kin(p(PFH:“PRKC Family”)) 1 17 4.2E-04 3.6E-04 0 2 163 19
kin(p(PFH:“MAPK p38 Family”)) 1 14 6.8E-09 4.9E-04 0 1 49 15
a(SCHEM:“Tetradecanoylphorbol acetate”) 1 16 2.5E-04 6.6E-04 0 2 144 18
bp(GO:“response to hypoxia”) 1 49 7.8E-05 9.1E-04 1 22 943 72
path(SDIS:“Photo-oxidative Stress”) 1 10 3.6E-06 9.8E-04 0 0 34 10
a(CHEBI:“arachidonic acid”) 1 15 2.6E-07 1.2E-03 0 2 80 17
tscript(p(HGNC:MEOX2)) −1 17 8.6E-10 1.3E-03 0 3 79 20
a(SCHEM:“Oxidized Low Density Lipoprotein”) 1 17 1.3E-04 1.3E-03 0 3 161 20
  1. Fifty-eight HYPs met richness and concordance thresholds of p < = 0.1 for data set GSE2638; the top twenty significant HYPs, as ranked by concordance are shown.