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.

MaturePred – Identification of microRNAs within novel Plant pre-miRNAs

MaturePred

:: DESCRIPTION

MaturePred web server can predict the start position of miRNA for a pre-miRNA candidate.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011;6(11):e27422. doi: 10.1371/journal.pone.0027422.
MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs.
Xuan P, Guo M, Huang Y, Li W, Huang Y.

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.

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

Mickael Leclercq (mickael.leclercq@mail.mcgill.ca)

:: 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.

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

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.

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.

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.

miRNAMap 2.0 – Genomic Maps of microRNAs in Metazoan Genomes

miRNAMap 2.0

:: DESCRIPTION

miRNAMap is a resource to collect experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3′ -UTR of genes.

::DEVELOPER

Integrative System Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.
Hsu SD, Chu CH, Tsou AP, Chen SJ, Chen HC, Hsu PW, Wong YH, Chen YH, Chen GH, Huang HD.
Nucleic Acids Res. 2008 Jan;36(Database issue):D165-9.

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S, Hofacker IL.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D135-9