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Table 1 Resources to construct a reliable miRNA-target protein network

From: Computational developments in microRNA-regulated protein-protein interactions

Name Process Main feature URL Ref.
BioGrid 2.1 Protein-protein interaction database [46]
Cytoscape Platform Social or molecular networks analysis and visualization. [47]
Database of Interacting Proteins (DIP) 2.1 Protein-protein interaction [48]
Ingenuity system Platform Signalling and metabolic pathways analysis; molecular network analysis etc.  
Human Protein Reference Database (HPRD) 2.1 Protein-protein interaction [49]
String 2.1 Protein-protein interaction [50]
The MIPS mammalian protein-protein interaction database 2.1 protein-protein interaction [51]
Protein Interaction Network Analysis (PINA) 2.2 PPI network construction, filtering, analysis, visualization and management [52]
HitPredict 2.1 Integrated PPI database [53]
iRefIndex 2.1 Integrated PPI database [54]
SynechoNET 1.1 Integrated PPI database [55]
PMRD 1.1 Plant miRNA database [56]
Gene ontology Platform Gene annotation, develop controlled vocabulary of genes [57]
MiRTarBase Platform miRNA-target interactions [58]
PicTar 1.2 miRNA target prediction [59]
RNAhybrid 1.2 miRNA target prediction [60]
TargetScan 1.2 miRNA target prediction [61]
GeneSet-2miRNA 1.2 miRNA target predicting with mRNA expression profile [62]
MMIA 1.2 miRNA target predicting with mRNA expression profile [63]
miRanda 1.2 miRNA target predicting & miRNA expression profiles [64]
MiRTif 1.4 miRNA target interaction filter [65]
miRBase 1.1 miRNA sequences and annotations [66]
The human microRNA disease database (HMDD) 1.1 miRNA sequences and annotations [49]
miRExpress 1.1 Extract miRNA expression profiles based on HTS results [67]
TarBase 1.2 Experimental supported miRNA target [68]
miRDeep 1.1 Detect novel miRNA based on HTS [69]
miRTools 1.1 Detect novel miRNA based on HTS [70]
starBase 1.3 Decoding microRNA-target and protein-RNA interaction [71]
IPA 1.4 Comprehensive software on biological analysis. Support miRNA target filtering