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

Gilles Caraux | Zendy; Sylvie Pinloche | Zendy

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

Author(s) -

Gilles Caraux,

Sylvie Pinloche

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti141

Subject(s) - computer science , cluster analysis , hierarchical clustering , graphical user interface , row , multidimensional scaling , data mining , expression (computer science) , tree (set theory) , row and column spaces , interface (matter) , seriation (archaeology) , biclustering , artificial intelligence , machine learning , mathematics , parallel computing , biology , fuzzy clustering , programming language , mathematical analysis , cure data clustering algorithm , paleontology , bubble , maximum bubble pressure method

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.

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