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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