mirConnX – Analysis of mRNA and microRNA (miRNA) Gene Regulatory Networks

mirConnX

:: DESCRIPTION

mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks. mirConnX combines sequence information, and computational predictions with gene expression data analysis to create a disease-specific, genome-wide regulatory network.

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W416-23. doi: 10.1093/nar/gkr276. Epub 2011 May 10.
mirConnX: condition-specific mRNA-microRNA network integrator.
Huang GT, Athanassiou C, Benos PV.

MIRPIPE 1.2.1 – miRNA detection and quantification pipeline

MIRPIPE 1.2.1

:: DESCRIPTION

MIRPIPE enables rapid and simple browser-based miRNA homology detection and quantification.

::DEVELOPER

the Loosolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MIRPIPE

:: MORE INFORMATION

Citation:

MIRPIPE – quantification of microRNAs in niche model organisms.
Kuenne C, Preussner J, Herzog M, Braun T, Looso M.
Bioinformatics. 2014 Aug 26. pii: btu573.

CCmiR – Prediction of miRNA Competitive / Cooperative Binding

CCmiR

:: DESCRIPTION

CCmiR is a software for competitive and cooperative microRNA binding prediction

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

CCmiR

:: MORE INFORMATION

Citation:

Bioinformatics. 2018 Jan 15;34(2):198-206. doi: 10.1093/bioinformatics/btx606.
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction.
Ding J, Li X, Hu H.

MITHrIL 1.0 – Mirna enrIched paTHway Impact anaLysis

MITHrIL 1.0

:: DESCRIPTION

MITHrIL (Mirna enrIched paTHway Impact anaLysis) is an algorithm developed for the analysis of signaling pathways. It extends pathways by adding missing regulatory elements, such as microRNAs, and their interactions with genes.

::DEVELOPER

MITHrIL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

MITHrIL

:: MORE INFORMATION

Citation:

Oncotarget. 2016 Aug 23;7(34):54572-54582. doi: 10.18632/oncotarget.9788.
Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification.
Alaimo S, Giugno R, Acunzo M, Veneziano D, Ferro A, Pulvirenti A.

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.