CN – Inferring Gene Regulatory Networks using SORDER algorithm

CN

:: DESCRIPTION

CN (Consensus Network) is a network inference method based on the SORDER algorithm and a suitable interval threshold for Conditional Mutual Information (CMI) tests

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 CN

:: MORE INFORMATION

Citation

CN: a consensus algorithm for inferring gene regulatory networks using the SORDER algorithm and conditional mutual information test.
Aghdam R, Ganjali M, Zhang X, Eslahchi C.
Mol Biosyst. 2015 Mar;11(3):942-9. doi: 10.1039/c4mb00413b

IPCA-CMI – Inferring Gene Regulatory Networks based on Combination of PCA-CMI and MIT score

IPCA-CMI

:: DESCRIPTION

IPCA-CMI is an algorithm for inferring gene regulatory networks based on a combination of PCA-CMI and MIT score.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 IPCA-CMI

:: MORE INFORMATION

Citation

PLoS One. 2014 Apr 11;9(4):e92600. doi: 10.1371/journal.pone.0092600. eCollection 2014.
IPCA-CMI: an algorithm for inferring gene regulatory networks based on a combination of PCA-CMI and MIT score.
Aghdam R1, Ganjali M1, Eslahchi C

LDGM – Identifying Gene Regulatory Network Rewiring using Latent Differential Graphical Models

LDGM

:: DESCRIPTION

LDGM estimates differential network between two tissue types directly without inferring the network for individual tissues.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

LDGM

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2016 Sep 30;44(17):e140. doi: 10.1093/nar/gkw581.
Identifying gene regulatory network rewiring using latent differential graphical models.
Tian D, Gu Q, Ma J.

ModEnt – Reconstructing Gene Regulatory Networks

ModEnt

:: DESCRIPTION

ModEnt is a computational tool that reconstructs gene regulatory networks from high throughput experimental data.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 ModEnt

:: MORE INFORMATION

Citation

Karlebach, G. and Shamir, R.,
Constructing logical models of gene regulatory networks by integrating transcription factor-DNA interactions with expression data: an entropy based approach.
Journal of Computational Biology.2012 Jan;19(1):30-41.

PTHGRN – Post-translational Hierarchal Gene Regulatory Network

PTHGRN

:: DESCRIPTION

PTHGRN is able to unravel interrelationships among PTMs, TFs, epigenetic modifications and gene expression and to reconstruct hierarchical gene regulatory networks underlying biological functions.

::DEVELOPER

Systems bioinformatics lab , Hong Kong Baptist University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data.
Guan D, Shao J, Zhao Z, Wang P, Qin J, Deng Y, Boheler KR, Wang J, Yan B.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W130-6. doi: 10.1093/nar/gku471. Epub 2014 May 29

LegumeGRN – Comparative Gene Regulatory Network Prediction Server

LegumeGRN

:: DESCRIPTION

LegumeGRN is a gene regulatory network (GRN) analysis tool for legume species. LegumeGRN provides a comprehensive, flexible and user-friendly web interface to build, test, analyse and visualize GRNs. It will help researchers to generate hypotheses about gene function and identify putative regulators of specific pathways for functional and comparative genomic studies.

::DEVELOPER

The Samuel Roberts Noble Foundation, Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2013 Jul 3;8(7):e67434. doi: 10.1371/journal.pone.0067434. Print 2013.
LegumeGRN: a gene regulatory network prediction server for functional and comparative studies.
Wang M1, Verdier J, Benedito VA, Tang Y, Murray JD, Ge Y, Becker JD, Carvalho H, Rogers C, Udvardi M, He J.

Netview – Explore the Human and Mouse Gene Regulatory Networks

Netview

:: DESCRIPTION

Netview is a free web tool that allow end users to explore the human and mouse gene regulatory networks. Users can query the system by providing a gene identifier and the boundaries of the subnetwork being explored. The system provides the list of interactions, the enriched Gene Ontology Terms together with a graphical representation of the subnetwork.

::DEVELOPER

di Bernardo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1101:179-96. doi: 10.1007/978-1-62703-721-1_10.
Reverse engineering transcriptional gene networks.
Belcastro V, di Bernardo D.

GPODE 20090927 – Learning Gene Regulatory Networks from Gene Expression Measurements

GPODE 20090927

:: DESCRIPTION

GPODE (GP4GRN) is a software of learning the structure of gene regulatory networks using non-parametric molecular kinetics. A set of Matlab functions that implement our gene regulatory network inference method. The method can use time-series and steady state gene expression (and protein) measurements and makes Bayesian inference for the network structure using Gaussian process based non-parametric molecular kinetics

::DEVELOPER

Tarmo Äijö

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Matlab

:: DOWNLOAD

 GPODE

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Nov 15;25(22):2937-44. Epub 2009 Aug 25.
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics.
Aijö T, Lähdesmäki H.

geneDBN V01.9R01 – Build Gene Regulatory Networks

geneDBN V01.9R01

:: DESCRIPTION

geneDBN is a software to build gene regulatory networks based on DBN (dynamic Bayesian network).

::DEVELOPER

Complex Computation Laboratory ,Iowa State University

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Registration First ; geneDBN

:: MORE INFORMATION

Copyright (C) 2007 Song Li and Hui-Hsien Chou.Bug report and suggestions are welcome and can be sent to geneDBN@www.complex.iastate.edu.

 

 

SpotXplore 20100804 – Cytoscape plugin for Visual Exploration of Hotspot Expression in Gene Regulatory Networks

SpotXplore 20100804

:: DESCRIPTION

SpotXplore is a plug-in for Cytoscape which enhances the visual analysis of gene expression obtained by, e.g., microarrays or the newer RNA-seq techniques in various ways. It enables visualization of multiple conditions or time series by glyphs that encode both expression value and statistical confidence.

::DEVELOPER

Dr. Michel A. Westenberg

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SpotXplore

:: MORE INFORMATION

Citation

M. A. Westenberg, J. B. T. M. Roerdink, O. P. Kuipers, S. A. F. T. van Hijum.
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.
Bioinformatics, 26(22):2922-2923, 2010.