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

:: 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

ReMoDiscovery – Inferring Transcriptional Module networks from ChIP-chip-, motif- and microarray data

ReMoDiscovery

:: DESCRIPTION

ReMoDiscovery is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way three independent data sources: ChIP-chip data, motif information and gene expression profiles.

::DEVELOPER

Kathleen Marchal

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

ReMoDiscovery

:: MORE INFORMATION

Citation

Genome Biol. 2006;7(5):R37. Epub 2006 May 5.
Inferring transcriptional modules from ChIP-chip, motif and microarray data.
Lemmens K, Dhollander T, De Bie T, Monsieurs P, Engelen K, Smets B, Winderickx J, De Moor B, Marchal K.

JCell 1.0.1 – A Java based framework for Inferring Genetic Networks

JCell 1.0.1

:: DESCRIPTION

JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ WIndows/MacOsX
Java

:: DOWNLOAD

JCell

:: MORE INFORMATION

Citation

JCell – a Java based framework for inferring regulatory networks from time series data
C. Spieth, J. Supper, F. Streichert, N. Speer, and A. Zell
Bioinformatics (2006) 22 (16): 2051-2052.