mirDIP : microRNA Data Integration Portal



References :

MicroRNA - target predictions

BCmicro

- Link: http://compgenomics.utsa.edu/gene/gene_1.php

- PMID: 23282032

 

Bi-Targeting (run 2021)

- Link: https://www.cs.bgu.ac.il/~vaksler/BiTargeting.htm

- PMID: 20465802

 

CoMeTa

- Link: http://cometa.tigem.it/index.php

- PMID: 22345618

 

Cupid (version 2015)

- Link: http://cupidtool.sourceforge.net/

- PMID: 25378249

 

DIANA

- Link: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index

- PMID: 22285563

 

MBStar (version 2014)

- Link: http://www.isical.ac.in/~bioinfo_miu/MBStar30.htm

- PMID: 25614300

 

mirAncestar (version 2016)

- Link: http://cs.mcgill.ca/~blanchem/mirancestar/

- PMID: 27899600

 

miRanda (run 2021)

- Link: http://www.microrna.org

- PMID: 15502875

 

miRbase (version 2014)

- Link: http://www.mirbase.org/

- PMID: 14681370

 

Mircode

- Link: http://www.mircode.org/index.php

- PMID: 22718787

 

mirCox (version 2013)

- Link: http://210.212.254.116/mircox/pages/index.php

- PMID: 24267917

 

miRDB (version 2019)

- Link: http://mirdb.org/

- PMID: 25378301

 

mirMAP (version 2013)

- Link: http://mirmap.ezlab.org/

- PMID: 23034802

 

miRNATIP (version 2016)

- Link: http://tblab.pa.icar.cnr.it/public/miRNATIP/1.0/

- PMID: 28185545

 

MirSNP

- Link: http://bioinfo.bjmu.edu.cn/mirsnp/download/

- PMID: 23173617

 

mirTar (version 2014)

- Link: http://mirtar.mbc.nctu.edu.tw/human/

- PMID: 21791068

 

miRTar2GO (version 2016)

- Link: http://mirtar2go.org/downloadPage.html

- PMID: 27903911

 

Mirza-G (version 2015)

- Link: http://www.clipz.unibas.ch/index.php?r=tools/sub/mirza_g

- PMID: 25628353

 

MultiMiTar (version 2014)

- Link: http://www.isical.ac.in/~bioinfo_miu/multimitar.htm

- PMID: 21949731

 

PACCMIT (version 2013)

- Link: http://lcpt.epfl.ch/MicroRNA_target_predictions

- PMID: 22915600

 

PITA (run 2021)

- Link: https://genie.weizmann.ac.il/pubs/mir07/

- PMID: 17893677

 

RNA22 (v2) (Ensembl 96 and miRBase 22)

- Link: https://cm.jefferson.edu/rna22/Interactive/

- Miranda,K.C., Huynh,T., Tay,Y., Ang,Y.S., Tam,W.L., Thomson,A.M., Lim,B. and Rigoutsos,I. (2006) A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes. Cell, 126, 1203?1217.

 

RNAhybrid (run 2021)

- Link: https://bibiserv2.cebitec.uni-bielefeld.de/rnahybrid

- PMID: 15383676

 

TargetScan 7.2 (2018)

- Link: http://www.targetscan.org/cgi-bin/targetscan/data_download.vert71.cgi

- PMID: 14697198

 

 

Tissue microRNA and gene expression

 

Bongiovanni*

-  mRNA Data: GSE126448

-  PMID: 31473989

 

Francisco*

-  miRNA data: GSE181922

-  PMID: 35482409

 

Ge*

-  miRNA and mRNA data: GSE121842

-  PMID: 31169949

 

GeW*

-  miRNA and mRNA data: GSE149084

 

GTEx

-  mRNA data: GTEx portal

-  PMID: 35549429

 

Hua*

-  miRNA data: GSE135055

-  PMID: 31902369

 

IID

-  mRNA data: IID website

-  PMID: 34755877

 

Kim*

-  mRNA data: GSE37765

-  PMID: 23405175

 

Lorenzi

- miRNA and mRNA data: GSE138734

- PMID: 34140680

 

Lyu*

-  miRNA and mRNA data: GSE137308

 

Mao*

-  mRNA data: GSE138518

-  PMID: 32759991

 

McCall

-  miRNA data: Supplementary Table 5

-  PMID: 28877962

 

Naccarati

-  miRNA data: GSE128359

-  PMID: 29423032

 

Panwar

-  miRNA data: Access via miRmine R-package http://bioconductor.org/packages/release/bioc/html/miRmine.html

-  PMID: 28108447

Rahman

-  miRNA data: GSE134949

 

Schulze

-  miRNA and mRNA data: GSE110719

-  PMID: 29986767

 

TCGA

-  miRNA and mRNA data: Firehose website

-  PMID: 29625045

 

Schulze

-  miRNA data: GSE110719

-  mRNA data: GSE110716

-  PMID: 29986767

 

Varghese*

-  miRNA data: GSE176288

-  mRNA data: GSE176271

-  PMID: 34557219

 

Vladimirova*

-  miRNA and mRNA data: GSE138042

-  PMID: 33748479

 

 

Novel microRNAs

 

-  Ali et al.

-  PMID: 32738291

 

-  Backes et al.

-  PMID: 26635395

 

-  Barros-Filho et al.

-  PMID: 30842597

 

-  De Rie et al.

-  PMID: 28829439

 

-  Fehlmann et al.

-  PMID: 28911107

 

-  Friedlšnder et al.

-  PMID: 24708865

 

-  Londin et al.

-  PMID: 25713380

 

- Lorenzi et al.

- PMID: 34140680

 

-  Martinez et al.

-  PMID: 31368811

 

-  McCall et al.

-  PMID: 28877962

 

-  Minatel et al.

-  PMID: 29587854

 

-  Pewarchuk et al.

-  PMID: 31739401

 

-  Rock et al.

-  PMID: 31828039

 

-  Wake et al.

-  PMID: 27716130




All contents copyright: Jurisica Lab, Schroeder Arthritis Institute, Krembil Research Institute - the University Health Network, Toronto, Canada. Last modified Sep 12, 2022. (Version 5.2.2.1, Database version 5.2.2.1)

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Reference:
- Tokar T, Pastrello C, Rossos AEM, Abovsky M, Hauschild AC, Tsay M, Lu R, Jurisica I. mirDIP 4.1-integrative database of human microRNA target predictions. Nucleic Acids Res. 2018 Jan 4;46(D1):D360-D370. doi: 10.1093/nar/gkx1144. PubMed PMID: 29194489; PubMed Central PMCID: PMC5753284
- Shirdel EA, Xie W, Mak TW, Jurisica I, 2011 NAViGaTing the Micronome. Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs. PLoS ONE 6(2): e17429. doi:10.1371/journal.pone.0017429