Table 1 Number of nodes, interactions and types of interactions in databases used to construct human integrated network. PPI: protein-protein interactions, TF: transcription factor
From: MasterPATH: network analysis of functional genomics screening data
Database | Nodes | Interactions | Types of nodes | Types of interactions | Direction of interactions |
|---|---|---|---|---|---|
HIPPIE (high confidence) | 9368 | 41,520 | proteins | PPI | undirected |
SIGNOR | 3977 | 13,129 | proteins, complexes, small molecules | PPI, enzymatic | directed, undirected |
SignaLink | 3285 | 27,295 | proteins, genes, miRNAs | PPI, miRNA-mRNA, TF-gene | directed, undirected |
TFactS | 2203 | 4312 | TFs, genes | TF-gene | directed |
KEGG metabolic pathways | 2921 | 8231 | proteins, small molecules | Enzymatic reactions | directed |
TransmiR | 324 | 647 | TFs, miRNAs | TF-miRNA | directed |
miRTarBase | 2269 | 3511 | miRNAs, genes | miRNA-mRNA | directed |