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