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Modular analysis of gene expression data with R

Csárdi, Gábor ; Kutalik, Zoltán ; Bergmann, Sven

In: Bioinformatics, 2010, vol. 26, no. 10, p. 1376-1377

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    Title
    • Modular analysis of gene expression data with R
    Author
    • Csárdi, Gábor. Department of Medical Genetics and Swiss Institute of Bioinformatics, University of Lausanne, Rue de Bugnon 27, CH-1005 Lausanne, Switzerland
    • Kutalik, Zoltán. Department of Medical Genetics and Swiss Institute of Bioinformatics, University of Lausanne, Rue de Bugnon 27, CH-1005 Lausanne, Switzerland
    • Bergmann, Sven. Department of Medical Genetics and Swiss Institute of Bioinformatics, University of Lausanne, Rue de Bugnon 27, CH-1005 Lausanne, Switzerland
    Document Type
    • Postprint
    OAI-PMH Identifier
    • oai:doc.rero.ch:295421
    Summary
    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