Skip to main content

Advertisement

Table 1 Enrichment of GO categories in gene modules. Enrichment of GO categories in gene modules obtained from (a) the human transcriptome dataset and (b) the soft tissue tumor dataset. Only functional categories containing at least 6 genes and p-values less than 0.01 are reported.

From: Biclustering of gene expression data by non-smooth non-negative matrix factorization

a)
Factor biological process #genes p-value
Factor 4 (726 genes) Neurogenesis 43 0.0
  Cell adhesion 33 1.30E-04
  Transport 32 0.003
  Synaptic transmission 31 0.0
  Regulation of transcription, DNA-dependent 25 0.0
  Central nervous system development 17 0.0
  Small GTPase mediated signal transduction 17 4.70E-04
  Potassium ion transport 11 0.008
  Sodium ion transport 10 2.40E-04
  Microtubule-based movement 9 0.0
  Neuropeptide signaling pathway 8 2.40E-04
  Regulation of apoptosis 8 0.009
  ATP synthesis coupled proton transport 6 0.001
  Microtubule polymerization 6 3.00E-05
  Vesicle-mediated transport 6 7.70E-04
Factor 5 (414 genes) Immune response 78 0.0
  Signal transduction 47 0.0
  Intracellular signaling cascade 29 0.0
  Inflammatory response 26 0.0
  Cellular defense response 21 0.0
  Antigen presentation, endogenous antigen 18 0.0
  Antigen processing, endogenous antigen via MHC class I 18 0.0
  Proteolysis and peptidolysis 17 0.003
  Cell motility 16 0.0
  Cell surface receptor linked signal transduction 15 0.0
  Chemotaxis 13 0.0
  Positive regulation of l-kappaB kinase/NF-kappaB cascade 13 0.0
  Regulation of apoptosis 12 0.0
  Heterophilic cell adhesion 11 0.0
  Antimicrobial tumoral response (sensu Vertebrata) 10 1.00E-05
  Small GTPase mediated signal transduction 10 0.004
  Anti-apoptosis 9 1.40E-04
  Defense response 8 7.00E-05
  Induction of apoptosis 8 0.002
  Response to virus 7 0.0
  Cell recognition 6 0.0
  Integrin-mediated signaling pathway 6 2.90E-04
Factor 8 (339 genes) Spermatogenesis 13 0.0
  Transcription 11 0.0
  Mitosis 6 0.002
b)
Factor biological process #genes p-value
Factor 1 (546 genes) Regulation of transcription, DNA-dependent 32 2.00E-05
  Development 16 0.003
  Neurogenesis 9 0.008
  Transcription from Pol II promoter 7 0.007
  Morphogenesis 6 0.002
  Skeletal development 6 0.007
  Chromosome organization and biogenesis (sensu Eukarya) 6 2.00E-05
Factor 2 (674 genes) Signal transduction 32 7.00E-05
  Immune response 30 0.0
  Cell adhesion 24 0.0
  Inflammatory response 17 0.0
  Chemotaxis 16 0.0
  Proteolysis and peptidolysis 15 0.002
  Cell growth and/or maintenance 13 0.002
  Cell-cell signaling 13 7.60E-04
  Cell proliferation 13 0.002
  Antimicrobial humoral response (sensu Vertebrata) 12 0.0
  G-protein coupled receptor protein signaling pathway 11 3.80E-04
  Cell motility 10 2.00E-05
  Cellular defense response 9 0.0
  Protein complex assembly 6 0.002
  Positive regulation of cell proliferation 6 0.008
  Cell-matrix adhesion 6 8.00E-05
  Blood coagulation 6 0.001
  Hetorophilic cell adhesion 6 0.002
Factor 3 (524 genes) Signal transduction 22 0.004
  Protein folding 6 0.002
Factor 4 (610 genes) Metabolism 16 1.00E-04
  Muscle development 11 1.00E-05
  Electron transport 10 0.005
  Carbohydrate metabolism 9 1.90E-04
  Muscle contraction 9 0.0
  DNA replication 6 0.002
  Energy pathways 6 4.20E-04
  Fatty acid metabolism 6 5.00E-05