Skip Navigation



Bioinformatics Advance Access published online on November 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti141
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/7/1280    most recent
bti141v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Caraux, G.
Right arrow Articles by Pinloche, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Caraux, G.
Right arrow Articles by Pinloche, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

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/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J DAIRY SCIHome page
S. Ollier, C. Leroux, A. de la Foye, L. Bernard, J. Rouel, and Y. Chilliard
Whole intact rapeseeds or sunflower oil in high-forage or high-concentrate diets affects milk yield, milk composition, and mammary gene expression profile in goats
J Dairy Sci, November 1, 2009; 92(11): 5544 - 5560.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Zeng and J. Li
Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways
Nucleic Acids Res., October 23, 2009; (2009) gkp822v1.
[Abstract] [Full Text] [PDF]

Home page
 J. Exp. Biol.Home page
N. I. Bower, X. Li, R. Taylor, and I. A. Johnston
Switching to fast growth: the insulin-like growth factor (IGF) system in skeletal muscle of Atlantic salmon
J. Exp. Biol., December 15, 2008; 211(24): 3859 - 3870.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
E. Dumas, B. Meunier, J.-L. Berdague, C. Chambon, M. Desvaux, and M. Hebraud
Comparative Analysis of Extracellular and Intracellular Proteomes of Listeria monocytogenes Strains Reveals a Correlation between Protein Expression and Serovar
Appl. Envir. Microbiol., December 1, 2008; 74(23): 7399 - 7409.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Endocrinol. Metab.Home page
N. K. Sharma, S. K. Das, A. K. Mondal, O. G. Hackney, W. S. Chu, P. A. Kern, N. Rasouli, H. J. Spencer, A. Yao-Borengasser, and S. C. Elbein
Endoplasmic Reticulum Stress Markers Are Associated with Obesity in Nondiabetic Subjects
J. Clin. Endocrinol. Metab., November 1, 2008; 93(11): 4532 - 4541.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
E. de la Vega, M. R. Hall, K. J. Wilson, A. Reverter, R. G. Woods, and B. M. Degnan
Stress-induced gene expression profiling in the black tiger shrimp Penaeus monodon
Physiol Genomics, September 11, 2007; 31(1): 126 - 138.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
T. Vuocolo, K. Byrne, J. White, S. McWilliam, A. Reverter, N. E. Cockett, and R. L. Tellam
Identification of a gene network contributing to hypertrophy in callipyge skeletal muscle
Physiol Genomics, February 12, 2007; 28(3): 253 - 272.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Reverter, A. Ingham, S. A. Lehnert, S.-H. Tan, Y. Wang, A. Ratnakumar, and B. P. Dalrymple
Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer
Bioinformatics, October 1, 2006; 22(19): 2396 - 2404.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.