Skip to main content

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 http://thebiogrid.org/ [46]
Cytoscape Platform Social or molecular networks analysis and visualization. http://www.cytoscape.org/ [47]
Database of Interacting Proteins (DIP) 2.1 Protein-protein interaction http://dip.doe-mbi.ucla.edu/dip/ [48]
Ingenuity system Platform Signalling and metabolic pathways analysis; molecular network analysis etc. http://www.ingenuity.com/  
Human Protein Reference Database (HPRD) 2.1 Protein-protein interaction http://www.hprd.org/ [49]
String 2.1 Protein-protein interaction http://string-db.org/ [50]
The MIPS mammalian protein-protein interaction database 2.1 protein-protein interaction http://mips.helmholtz-muenchen.de/proj/ppi/ [51]
Protein Interaction Network Analysis (PINA) 2.2 PPI network construction, filtering, analysis, visualization and management http://cbg.garvan.unsw.edu.au/pina/ [52]
HitPredict 2.1 Integrated PPI database http://hintdb.hgc.jp/htp/ [53]
iRefIndex 2.1 Integrated PPI database http://www.irefindex.org/wiki/index.php?title=iRefIndex [54]
SynechoNET 1.1 Integrated PPI database http://bioportal.kobic.re.kr/SynechoNET/ [55]
PMRD 1.1 Plant miRNA database http://bioinformatics.cau.edu.cn/PMRD/ [56]
Gene ontology Platform Gene annotation, develop controlled vocabulary of genes http://www.geneontology.org/ [57]
MiRTarBase Platform miRNA-target interactions http://mirtarbase.mbc.nctu.edu.tw/ [58]
PicTar 1.2 miRNA target prediction http://pictar.mdc-berlin.de/ [59]
RNAhybrid 1.2 miRNA target prediction http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ [60]
TargetScan 1.2 miRNA target prediction http://www.targetscan.org/ [61]
GeneSet-2miRNA 1.2 miRNA target predicting with mRNA expression profile http://mips.helmholtz-muenchen.de/proj/gene2mir/ [62]
MMIA 1.2 miRNA target predicting with mRNA expression profile http://129.79.244.122/~MMIA/ [63]
miRanda 1.2 miRNA target predicting & miRNA expression profiles http://www.microrna.org/ [64]
MiRTif 1.4 miRNA target interaction filter http://mirtif.bii.a-star.edu.sg/ [65]
miRBase 1.1 miRNA sequences and annotations http://www.mirbase.org/ [66]
The human microRNA disease database (HMDD) 1.1 miRNA sequences and annotations http://202.38.126.151/hmdd/mirna/md/ [49]
miRExpress 1.1 Extract miRNA expression profiles based on HTS results http://mirexpress.mbc.nctu.edu.tw/ [67]
TarBase 1.2 Experimental supported miRNA target http://diana.cslab.ece.ntua.gr/tarbase/ [68]
miRDeep 1.1 Detect novel miRNA based on HTS https://www.mdc-berlin.de/690237/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/index.html [69]
miRTools 1.1 Detect novel miRNA based on HTS http://centre.bioinformatics.zj.cn/mirtools/ [70]
starBase 1.3 Decoding microRNA-target and protein-RNA interaction http://starbase.sysu.edu.cn/ [71]
IPA 1.4 Comprehensive software on biological analysis. Support miRNA target filtering http://www.ingenuity.com/products/training.html