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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)