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Bioinformatics Advance Access originally published online on November 16, 2004
Bioinformatics 2005 21(7):1280-1281; doi:10.1093/bioinformatics/bti141
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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

Gilles Caraux 1,2,3,* and Sylvie Pinloche 1

1Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier 161 rue Ada, 34392 Montpellier cedex 5, France
2Ecole Nationale Supérieure Agronomique de Montpellier 2, Place P.Viala, 34060 Montpellier Cedex 02, France
3Research School of Biological Sciences, Australian National University Canberra, Australia

*To whom correspondence should be addressed.

Summary: PermutMatrix is a work space designed to graphically explore gene expression data. It relies on the graphical approach introduced by Eisen 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 that 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/

Contact: caraux{at}lirmm.fr


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