Journal Article

Modular analysis of gene expression data with R

Gábor Csárdi, Zoltán Kutalik and Sven Bergmann

in Bioinformatics

Volume 26, issue 10, pages 1376-1377
Published in print May 2010 | ISSN: 1367-4803
Published online April 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq130
Modular analysis of gene expression data with R

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Summary: Large sets of data, such as expression profiles from many samples, require analytic tools to reduce their complexity. The Iterative Signature Algorithm (ISA) is a biclustering algorithm. It was designed to decompose a large set of data into so-called ‘modules’. In the context of gene expression data, these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments. Genes and arrays may be attributed to multiple modules and the level of required coherence can be varied resulting in different ‘resolutions’ of the modular mapping. In this short note, we introduce two BioConductor software packages written in GNU R: The isa2 package includes an optimized implementation of the ISA and the eisa package provides a convenient interface to run the ISA, visualize its output and put the biclusters into biological context. Potential users of these packages are all R and BioConductor users dealing with tabular (e.g. gene expression) data.

Availability: http://www.unil.ch/cbg/ISA

Contact: sven.bergmann@unil.ch

Journal Article.  1222 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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