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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

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

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