ViTraM 2.0 – Visualization of Transcriptional Modules

ViTraM 2.0

:: DESCRIPTION

ViTraM (Visualization of Transcriptional Modules) is a flexible software platform for visualizing overlapping transcriptional modules in an intuitive way. By visualizing not only the genes and the experiments in which the genes are co-expressed, but also additional properties of the modules such as the regulators and regulatory motifs that are responsible for the observed co-expression, ViTraM can assist in the biological analysis and interpretation of the output of module detection tools.

::DEVELOPER

Kathleen Marchal

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

ViTraM

:: MORE INFORMATION

Citation

H. Sun, K. Lemmens, T. Van den Buckle, K. Engelen, B. De Moor, K. Marchal.
“ViTraM: Visualization of Transcriptional Modules” (2009).
Bioinformatics, 25(18):2450-2451;

Arboretum – Reconstruction and analysis of Evolutionary History of Condition-specific Transcriptional Modules

Arboretum

:: DESCRIPTION

Arboretum is a novel scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories.

::DEVELOPER

Roy Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Arboretum

:: MORE INFORMATION

Citation

Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.
Roy S, Wapinski I, Pfiffner J, French C, Socha A, Konieczka J, Habib N, Kellis M, Thompson D, Regev A.
Genome Res. 2013 Jun;23(6):1039-50. doi: 10.1101/gr.146233.112.

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.