ExpressionView - an interactive viewer for modules identified in gene expression data

SUMMARY ExpressionView is an R package that provides an interactive graphical environment to explore transcription modules identified in gene expression data. A sophisticated ordering algorithm is used to present the modules with the expression in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual modules and access biologically relevant metadata associated with them. AVAILABILITY http://www.unil.ch/cbg/ExpressionView. Screenshots, tutorials and sample data sets can be found on the ExpressionView web site.

[1]  Arlindo L. Oliveira,et al.  Biclustering algorithms for biological data analysis: a survey , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[2]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[3]  Sven Bergmann,et al.  Challenges and prospects in the analysis of large-scale gene expression data , 2004, Briefings Bioinform..

[4]  E. Ziegel.  COMPSTAT: Proceedings in Computational Statistics , 1988 .

[5]  T. M. Murali,et al.  Automatic layout and visualization of biclusters , 2006, Algorithms for Molecular Biology.

[6]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[7]  Lothar Thiele,et al.  A systematic comparison and evaluation of biclustering methods for gene expression data , 2006, Bioinform..

[8]  Sven Bergmann,et al.  Iterative signature algorithm for the analysis of large-scale gene expression data. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[9]  Sven Bergmann,et al.  Modular analysis of gene expression data with R , 2010, Bioinform..

[10]  Friedrich Leisch,et al.  A toolbox for bicluster analysis in R , 2008 .

[11]  Wan-Chi Siu,et al.  BiVisu: software tool for bicluster detection and visualization , 2007, Bioinform..

[12]  Roberto Therón,et al.  BicOverlapper: A tool for bicluster visualization , 2008, Bioinform..

[13]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.