Table 4 Description of the biological role of an illustrative set of BicNET’s modules with varying properties
From: BicNET: Flexible module discovery in large-scale biological networks using biclustering
|  | ID | Homogeneity | \(\sharp\)Nodes \(|I|\times |J|\) | Putative functionality: group of enriched terms (\(p<\)1E−10) |
|---|---|---|---|---|
STRING (yeast) | Y1 | Dense (high noise-tolerance) | 231 × 14 | Metabolic processes with incidence on protein, peptide and amide metabolism and biosynthesis |
Y2 | Dense (medium noise-tolerance) | 217 × 9 | Metabolism of nitrogen compounds and some organic substances | |
Y3 | Constant (few high \(a_{ij}\)) | 103 × 8 | Amino acid activation and tRNA metabolism for tRNA aminoacylation | |
Y4 | Constant (few high \(a_{ij}\)) | 206 × 6 | Organic acid metabolic process and its subterms | |
Y5 | Constant (few high or low \(a_{ij}\)) | 55 × 7 | Signal transduction and its subterms | |
Y6 | Constant (few high or low \(a_{ij}\)) | 43 × 6 | Phosphorylation related terms (with incidence on protein phosphorylation) | |
Y7 | Order-preserving | 176 × 12 | Transport of organic acids (with incidence on aminoacid transmembrane transport) | |
Y8 | Order-preserving | 235 × 9 | Oxidation-reduction process and metabolism of aminoacids. Assembly of ribonucleoprotein | |
Y9 | Order-pres. (few high \(a_{ij}\)) | 146 × 8 | Transport of molecules (highest enrichment found for drug transmembrane) | |
STRING (human) | H1 | Dense (high noise-tolerance) | 811 × 28 | Multiple metabolic processes with incidence on transcription activity |
H2 | Dense (high noise-tolerance) | 787 × 25 | Regulation of metabolic processes (both positive and negative regulation) | |
H3 | Constant (few high \(a_{ij}\)) | 693 × 14 | Regulation of intracellular signal transduction (over 20 highly enriched terms) | |
H4 | Constant (few high \(a_{ij}\)) | 645 × 10 | Regulation of molecular functions (incidence on catalytic activity) | |
H5 | Order-preserving | 720 × 24 | Establishment of protein localization (protein targeting to ER and membrane) | |
H6 | Order-preserving | 733 × 29 | Protein phosphorylation and its subterms | |
DryGIN | D1 | Dense (high noise-tolerance) | 28 × 17 | Organelle localization (establishment of spindle and nuclear localization) |
D2 | Constant (with pos&neg \(a_{ij}\)) | 22 × 10 | Chromatin remodeling and nucleosome organization | |
D3 | Constant (with pos&neg \(a_{ij}\)) | 21 × 7 | Transport processes for the establishment of protein localization | |
D4 | Constant (with pos&neg \(a_{ij}\)) | 19 × 9 | Regulation of growth (incidence on filamentous growth) | |
D5 | Order-preserving | 39 × 7 | Organelle and nucleous organization | |
D6 | Order-preserving | 54 × 6 | Regulation of cellular metabolic processes (both positive and negative regulation) |