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 |