Table 9 Biological role of a subset of BicPAMS’ modules with varying properties
From: BicPAMS: software for biological data analysis with pattern-based biclustering
|  | ID | Homogeneity | ♯Nodes |I|×|J| | Putative biological functions: enriched terms (p<1E-10) |
|---|---|---|---|---|
STRING (yeast) | Y1 | dense (high noise-tolerance) | 231 ×14 | Metabolic processes with incidence on peptide, protein and amide metabolism and biosynthesis. |
|  | Y2 | dense (medium noise-tolerance) | 217 ×9 | Metabolism of nitrogen compounds and other organic substances. |
|  | Y3 | constant (few high a ij ) | 103 ×8 | Amino acid activation and tRNA metabolism for aminoacylation. |
|  | Y4 | constant (few high or low a ij ) | 55 ×7 | Signal transduction and its related subterms. |
|  | Y5 | constant (few high or low a ij ) | 43 ×6 | Phosphorylation terms (with more incidence on protein phosphorylation). |
|  | Y6 | order-preserving | 176 ×12 | Transport of organic acids (incidence on aminoacid transmembrane transport). |
|  | Y7 | order-preserving | 235 ×9 | Oxidation-reduction process and metabolism of aminoacids. |
|  | Y8 | 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 | constant (few high a ij ) | 693 ×14 | Regulation of intracellular signal transduction (over twenty highly enriched terms). |
|  | H3 | constant (few high a ij ) | 645 ×10 | Regulation of molecular functions with incidence on catalytic activity. |
|  | H4 | order-preserving | 720 ×24 | Establishment of protein localization (protein targeting to ER and membrane). |
|  | H5 | 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 (with incidence on filamentous growth). |
|  | D5 | order-preserving | 39 ×7 | Organelle and nucleous organization. |
|  | D6 | order-preserving | 54 ×6 | Negative and positive regulation of cellular metabolic processes. |