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Bioinformatics Advance Access published online on November 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti141
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 10, 2004
Revised September 3, 2004
Accepted October 4, 2004

Applications note

PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order

Gilles Caraux 1* and Sylvie Pinloche 2

1 Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier, 161 rue Ada, 34392 Montpellier cedex 5, France; Ecole Nationale Supérieure Agronomique de Montpellier, 2, Place P.Viala, 34060 Montpellier Cedex 02, France; Research School of Biological Sciences, Australian National University, Canberra, Australia
2 Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier, 161 rue Ada, 34392 Montpellier cedex 5, France

* To whom correspondence should be addressed.
Gilles Caraux, E-mail: caraux{at}lirmm.fr


  Abstract

PermutMatrix is a work space designed to graphically explore gene expression data. It relies on the graphical approach introduced by Eisen (Eisen et al., 1998), and also offers several methods for the optimal reorganization of rows and columns of a numerical dataset. For example, several methods are proposed for optimal reorganization of the leaves of a hierarchical clustering tree, along with several seriation or unidimensional scaling methods which do not require any preliminary hierarchical clustering. This program, developed for MS Windows, with MS-Visual C++, has a clear and efficient graphical interface. Large datasets can be thoroughly and quickly analyzed.

Availability: http://www.lirmm.fr/~caraux/PermutMatrix/.


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