GemiNI – Network based integration of Gene Expression profiles with miRNA Expression Profiles

GemiNI

:: DESCRIPTION

GemiNI /dChip-GemiNi (Gene and miRNA Network-based Integration) is a web server which is an integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops

::DEVELOPER

Cheng Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GemiNI

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep 1;40(17):e135.
Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers.
Yan Z, Shah PK, Amin SB, Samur MK, Huang N, Wang X, Misra V, Ji H, Gabuzda D, Li C.

HDMP – Human Disease-related miRNA Prediction

HDMP

:: DESCRIPTION

HDMP can predict the disease-related miRNA candidates for 18 human diseases.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2013 Aug 8;8(8):e70204. doi: 10.1371/journal.pone.0070204. eCollection 2013.
Prediction of microRNAs associated with human diseases based on weighted k most similar neighbors.
Xuan P, Han K, Guo M, Guo Y, Li J, Ding J, Liu Y, Dai Q, Li J, Teng Z, Huang Y.

SplamiR – Predicting miRNAs in Plants

SplamiR

:: DESCRIPTION

SplamiR is the first method for the prediction of spliced miRNAs in plants. It takes genomic sequence and the sequence of a potential target mRNA as input. In the first phase of SplamiR, a database of complementary sequence pairs is created for the given genomic sequence. These sequence pairs might encode for RNAs folding into stem-loop structures. In the second phase, this database is searched for sequences with complementarity to the given target mRNA. For the identified sequences, in silico splice variants are generated and these are classified as to whether they might represent pre-miRNAs.

::DEVELOPER

Theißen lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

  SplamiR

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 May 1;27(9):1215-23. doi: 10.1093/bioinformatics/btr132. Epub 2011 Mar 17.
SplamiR–prediction of spliced miRNAs in plants.
Thieme CJ, Gramzow L, Lobbes D, Theissen G.

miFRame – Analysis and Visualization of miRNA sequencing data in Neurological Disorders

miFRame

:: DESCRIPTION

miFRame which supports the analysis of human small RNA NGS data is a web server for analysis and visualization of miRNA sequencing data in neurological disorders.

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Transl Med. 2015 Jul 14;13:224. doi: 10.1186/s12967-015-0594-x.
miFRame: analysis and visualization of miRNA sequencing data in neurological disorders.
Backes C, Haas J, Leidinger P, Frese K, Großmann T, Ruprecht K, Meder B, Meese E, Keller A

MirCompare – Algorithm to Compare Plant and Mammalian miRNAs

MirCompare

:: DESCRIPTION

MirCompare is an innovative algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs.

::DEVELOPER

MirCompare team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction.
Pirrò S, Minutolo A, Galgani A, Potestà M, Colizzi V, Montesano C.
J Comput Biol. 2016 Jul 18.

miRNAFold – Ab initio miRNA Precursor Search in Genomes

miRNAFold

:: DESCRIPTION

miRNAFold is a fast ab-initio algorithm for searching for pre-miRNA precursors in genomes.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miRNAFold: a web server for fast miRNA precursor prediction in genomes.
Tav C, Tempel S, Poligny L, Tahi F.
Nucleic Acids Res. 2016 May 29. pii: gkw459.

Nucleic Acids Res. 2012 Jun;40(11):e80. doi: 10.1093/nar/gks146. Epub 2012 Feb 22.
A fast ab-initio method for predicting miRNA precursors in genomes.
Tempel S1, Tahi F.

miRlastic 1.0 – Integrative Analysis of miRNA and mRNA Expression data

miRlastic 1.0

:: DESCRIPTION

miRlastic is a novel method  which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network.

::DEVELOPER

Computational Cell Maps Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

 miRlastic

:: MORE INFORMATION

Citation

MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma.
Sass S, Pitea A, Unger K, Hess J, Mueller NS, Theis FJ.
Int J Mol Sci. 2015 Dec 18;16(12):30204-22. doi: 10.3390/ijms161226230.

miRNA Digger – Genome-wide novel miRNA Mining

miRNA Digger

:: DESCRIPTION

miRNA Digger is a pipeline for large-scale identifiction of the new microRNA genes by screening the cleavage signals resided within the genome.

::DEVELOPER

miRNA Digger team

:: SCREENSHOTS

miRNADigger

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 miRNA Digger

:: MORE INFORMATION

Citation:

miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.
Yu L, Shao C, Ye X, Meng Y, Zhou Y, Chen M.
Sci Rep. 2016 Jan 6;6:18901. doi: 10.1038/srep18901.

miR-isomiRExp – Analysis of Expression of miRNA at the miRNA/isomiR levels

miR-isomiRExp

:: DESCRIPTION

miR-isomiRExp is an approach to analyze expression pattern of miRNA at the miRNA/isomiR levels, provide insights into tracking miRNA/isomiR maturation and processing mechanisms, and reveal functional characteristics of miRNA/isomiR.

::DEVELOPER

miR-isomiRExp team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 miR-isomiRExp

:: MORE INFORMATION

Citation

miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels.
Guo L, Yu J, Liang T, Zou Q.
Sci Rep. 2016 Mar 24;6:23700. doi: 10.1038/srep23700.

MatureBayes – Web-based tool for the Computational Identification of Mature miRNAs

MatureBayes

:: DESCRIPTION

MatureBayes is a tool for finding mature miRNA within a miRNA precursor sequence using a Naive Bays classifier.

::DEVELOPER

Computational Biology Lab, IMBB/FORTH

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MatureBayes

:: MORE INFORMATION

Citation

MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors.
Gkirtzou K, Tsamardinos I, Tsakalides P, Poirazi P.
PLoS One. 2010 Aug 6;5(8):e11843. doi: 10.1371/journal.pone.0011843.