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A Java Package for Microarray Data Visualisation and Analysis (Version 1.4 - Updated on 05/15/2009).

Ghislain Bidaut (Updated the 15/05/09).
Integrative Bioinformatics - Centre de Recherche en Cancérologie de Marseille,
Institut National de la Santé et de la Recherche Médicale, INSERM UMR 891
27 Boulevard Leï Roure, 13009, Marseille, France
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Introduction

ClutrFree allows the visualization and interpretation of gene expression data clusters for multiple clustering experiments. Data is integrated with ontological annotations (GO), and enrichement of annotations (hypergeometric distribution) is computed.
ClutrFree facilitates the visualization and interpretation of clusters or patterns computed from microarray data through a graphical user interface that displays patterns, membership information of the genes and annotation statistics simultaneously. ClutrFree creates a tree linking the patterns based on similarity, permitting the navigation among patterns identified by different algorithms or by the same algorithm with different parameters, and aids the inferring of conclusions from a microarray experiment. The ClutrFree Java source code and compiled bytecode are available as a package under the GNU General Public License.

News

  • 05/15/2009: new ClutrFree release (Version 1.4 - fixed bugs with the MEV data plugin reader).
  • 02/14/2008: new ClutrFree release (1.26 - this is a bugfix only release).
  • 02/14/2008: new ClutrFree Web Site on Sourceforge!

Test Datasets

Schmidt cancer microarray dataset (Analysis with TMEV implementation of K-means - from 3 to 20 patterns)
Phylogenomic profiles Dataset (Analysis with Bayesian Decomposition - Pattools implementation)
Rosetta Yeast Compendium Dataset (Analysis with Bayesian Decomposition - Pattools implementation)

Clutrfree Publications

  • Bidaut G. (in preparation). Interpreting multiple microarray clustering experiments with the ClutrFree package Methods Mol Biol. 2009. (Supplementary data)
  • Bidaut G. (2007): Gene function inference from gene expression of deletion mutants. Methods Mol Biol. 2007;408:1-18. [PMID: 18314574] (supplementary data)
  • Bidaut G & Ochs MF (2004): ClutrFree: cluster tree visualization and interpretation. Bioinformatics. 2004 Nov 1;20(16):2869-71.[PMID: 15145813]

Questions? Comments ? Please do not hesitate to contact us (from the ClutrFree Page on SourceForge)
This page is copyrighted (c)Ghislain Bidaut 2009.