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Table 2 Summarizing the inferred melanoma cancer clusters

From: Identifying pathogenic processes by integrating microarray data with prior knowledge

Cluster Size Upreg. (%) Edges Priors (%) Top three GO terms
1 130 2.3 16770 1.3 Epidermis development, cornified envelope, keratinization
2 25 4.0 600 0.0 Androgen biosynthetic process, extracellular region, desmosome
3 28 3.6 756 1.7 Forebrain morphogenesis, response to vitamin A, negative regulation of neuron maturation
4 25 0.0 600 1.2 Keratinization, peptide cross-linking, desmosome
5 17 52.9 272 1.8 Testosterone 16-alpha-hydroxylase activity, negative regulation of Rho GTPase activity,
      negative regulation of epidermal growth factor-activated receptor activity
6 13 61.5 156 1.9 Alcohol sulfotransferase activity, CDP-diacylglycerol biosynthetic process, embryonic
      hindgut morphogenesis
7 13 53.8 156 1.3 Regulation of mesonephros development, negative regulation of cell proliferation involved
      in mesonephros development, negative regulation of fibroblast growth factor receptor
      signaling pathway involved in ureteric bud formation
8 12 0.0 132 0.0 Glutamate dehydrogenase (NAD+) activity, glutamate dehydrogenase [NAD(P)+] activity,
      negative regulation of myelination
9 12 16.7 132 1.5 Serine-type endopeptidase activity, serine hydrolase activity, peptidase activity, acting on
      L-amino acid peptides
10 10 50.0 90 0.0 Adherens junction organization,interleukin-1 Type I receptor binding, dihydrotestosterone
      17-beta-dehydrogenase activity
11 10 0 90 1.1 N-acylglucosamine 2-epimerase activity, osteoclast proliferation, alkaloid catabolic process
12 10 30.0 90 0.0 Middle ear morphogenesis, vagus nerve morphogenesis, activation of phospholipase
      D activity by G-protein coupled receptor protein signaling pathway
13 11 9.1 110 0.9 Scavenger receptor activity, negative regulation of collateral sprouting of intact axon
      in response to injury, regulation of cell adhesion
14 11 0.0 110 0.9 Positive regulation of cell development, regulation of cell morphogenesis involved in
      differentiation, argininosuccinate synthase activity
15 12 16.7 132 0.0 Pharynx development, cellular response to external biotic stimulus, nucleus
16 9 0.0 72   1.4 Alpha-dystroglycan binding, isopeptide cross-linking via N6-(L-isoglutamyl)-L lysine,
      positive regulation of arachidonic acid secretion
17 7 100.0 42 14.3 Vascular transport, interleukin-1 Type II blocking receptor activity, Golgi cis cisterna
18 6 66.7 30 3.3 NLRP1 inammasome complex, 17-alpha,20-alpha-dihydroxypregn-4-en-3-one
      dehydrogenase activity, androsterone dehydrogenase (B-specific) activity
  1. Size = number of genes in each cluster, Upreg. (%) = percentage of upregulated genes, Edges = number of edges, Priors (%) = percentage of edges that were prior pairs, and Top three GO terms = the three most significant Gene Ontology terms found by GOstats [33].