CORNA 1.3 – Testing Gene Lists for Regulation by microRNAs

CORNA 1.3

:: DESCRIPTION

CORNA is a package for R that analyses microarray data and miRNA target prediction data to find statistically over-represented miRNA-target relationships.

::DEVELOPER

CORNA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 CORNA

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 15;25(6):832-3. doi: 10.1093/bioinformatics/btp059. Epub 2009 Jan 29.
CORNA: testing gene lists for regulation by microRNAs.
Wu X1, Watson M.

miR-AT! 1.6 – Prediction of Combinatorial Activity of microRNAs

miR-AT! 1.6

:: DESCRIPTION

miR-AT! is a computational tool for the identification of all transcripts that are targets of a list of input miRNAs.

::DEVELOPER

Dombkowski Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Dombkowski A.A., Sultana, Z., Craig, D.B., Jamil, H.,
In silico analysis of combinatorial microRNA activity reveals target genes and pathways associated with breast cancer metastasis.
Cancer Informatics, 2011;10:13-29

miRror 2.0 – A Dual View on Sets of MicroRNAs and their Targets

miRror 2.0

:: DESCRIPTION

miRror Suite is an analysis tools for the cooperative regulation by microRNAs on gene sets and pathways

PSI-miRror: Probability Supported Iterative miRror

::DEVELOPER

miRror team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Database (Oxford). 2014 Jun 6;2014. pii: bau043. doi: 10.1093/database/bau043. Print 2014.
miRror-Suite: decoding coordinated regulation by microRNAs.
Friedman Y, Karsenty S, Linial M

J Bioinform Comput Biol. 2013 Dec;11(6):1343012. doi: 10.1142/S0219720013430129.
miRror2.0: a platform for assessing the joint action of microRNAs in cell regulation.
Friedman Y, Linial M.

MIReNA 2.0 – Find microRNAs with high Accuracy and No Learning

MIReNA 2.0

:: DESCRIPTION

MIReNA is a tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. MIReNA validates pre-miRNAs with high sensitivity and specificity, and detects new miRNAs by homology from known miRNAs or from deep sequencing data.

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl
  • Python
  • RNAfold

:: DOWNLOAD

 MIReNA

:: MORE INFORMATION

Citation

A. Mathelier and A. Carbone. (2010)
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.
Bioinformatics. 10.1093/bioinformatics/btq329

miRSel – Automated Extraction of Associations between microRNAs and Genes from the Biomedical Literature

miRSel

:: DESCRIPTION

miRSel is resource for miRNA-gene associations. miRSel offers the currently largest collection of literature derived miRNA-gene associations.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Mar 16;11:135. doi: 10.1186/1471-2105-11-135.
miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature.
Naeem H, Küffner R, Csaba G, Zimmer R.

MiRdup 1.4 – Prediction of the Localization of microRNAs within their pre-miRNA

MiRdup 1.4

:: DESCRIPTION

miRdup is a computational predictor for the identification of the most likely miRNA location within a given pre-miRNA or the validation of a candidate miRNA.

::DEVELOPER

Mathieu Blanchette’sComputational Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MiRdup

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Aug;41(15):7200-11. doi: 10.1093/nar/gkt466. Epub 2013 Jun 8.
Computational prediction of the localization of microRNAs within their pre-miRNA.
Leclercq M1, Diallo AB, Blanchette M.

miR2GO – Comparative Functional analysis for microRNAs

miR2GO

:: DESCRIPTION

miR2GO is a web based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO (Functional analysis of genetic and somatic mutations in microRNAs) and miRpair2GO (Comparative functional analysis for microRNA pairs).

::DEVELOPER

Yan Cui’s Lab at University of Tennessee Health Science Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

miR2GO: Comparative functional analysis for microRNAs.
Bhattacharya A, Cui Y.
Bioinformatics. 2015 Mar 10. pii: btv140.

EdgeExpressDB 0.954 – Integrated database of Promoters, Genes, microRNAs, Expression Dynamics and Regulatory Interactions.

EdgeExpressDB 0.954

:: DESCRIPTION

EdgeExpressDB (eeDB) is a federated data abstraction system designed for integrating, interpreting, and visualizing very large biology datasets.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux
  • Perl DBI/DBD, MySQL, SQLite.

:: DOWNLOAD

 EdgeExpressDB

:: MORE INFORMATION

Citation

Genome Biol. 2009;10(4):R39. doi: 10.1186/gb-2009-10-4-r39. Epub 2009 Apr 19.
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.
Severin J1, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR.

OncomiRDB – Database for the Experimentally Verified Oncogenic and Tumor-suppressive microRNAs

OncomiRDB

:: DESCRIPTION

OncomiRDB is a web-based portal, which provides both graphical and text-based interfaces, was developed for easily browsing and searching all the annotations. It should be a useful resource for both the computational analysis and experimental study on miRNA regulatory networks and functions in cancer.

::DEVELOPER

Bioinformatics & Intelligent Information Processing Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 N/A

:: MORE INFORMATION

Citation

OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs.
Bioinformatics 2014, 30(15):2237-2238.
Dongfang Wang, Jin Gu#, Ting Wang, Zijian Ding.

miRMaid 1.0 – microRNAs data structured for easier access and integration

miRMaid 1.0

:: DESCRIPTION

miRMaid is an intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 miRMaid

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Jan 14;11:29. doi: 10.1186/1471-2105-11-29.
miRMaid: a unified programming interface for microRNA data resources.
Jacobsen A, Krogh A, Kauppinen S, Lindow M.