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. | Â | |
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 | Â |