Literature DB >> 18321885

BicOverlapper: a tool for bicluster visualization.

Rodrigo Santamaría1, Roberto Therón, Luis Quintales.   

Abstract

UNLABELLED: BicOverlapper is a tool to visualize biclusters from gene-expression matrices in a way that helps to compare biclustering methods, to unravel trends and to highlight relevant genes and conditions. A visual approach can complement biological and statistical analysis and reduce the time spent by specialists interpreting the results of biclustering algorithms. The technique is based on a force-directed graph where biclusters are represented as flexible overlapped groups of genes and conditions. AVAILABILITY: The BicOverlapper software and supplementary material are available at http://vis.usal.es/bicoverlapper

Mesh：

Year:  2008        PMID： 18321885     DOI： 10.1093/bioinformatics/btn076

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  11 in total

Review 1.  Visualization of omics data for systems biology.

Authors:  Nils Gehlenborg; Seán I O'Donoghue; Nitin S Baliga; Alexander Goesmann; Matthew A Hibbs; Hiroaki Kitano; Oliver Kohlbacher; Heiko Neuweger; Reinhard Schneider; Dan Tenenbaum; Anne-Claude Gavin
Journal:  Nat Methods       Date:  2010-03       Impact factor: 28.547

2.  Recursive expectation-maximization clustering: a method for identifying buffering mechanisms composed of phenomic modules.

Authors:  Jingyu Guo; Dehua Tian; Brett A McKinney; John L Hartman
Journal:  Chaos       Date:  2010-06       Impact factor: 3.642

3.  iBBiG: iterative binary bi-clustering of gene sets.

Authors:  Daniel Gusenleitner; Eleanor A Howe; Stefan Bentink; John Quackenbush; Aedín C Culhane
Journal:  Bioinformatics       Date:  2012-07-12       Impact factor: 6.937

4.  Methods for visual mining of genomic and proteomic data atlases.

Authors:  John Boyle; Richard Kreisberg; Ryan Bressler; Sarah Killcoyne
Journal:  BMC Bioinformatics       Date:  2012-04-23       Impact factor: 3.169

5.  Discovery and visualization of miRNA-mRNA functional modules within integrated data using bicluster analysis.

Authors:  Kenneth Bryan; Marta Terrile; Isabella M Bray; Raquel Domingo-Fernandéz; Karen M Watters; Jan Koster; Rogier Versteeg; Raymond L Stallings
Journal:  Nucleic Acids Res       Date:  2013-12-18       Impact factor: 16.971

6.  SiBIC: a web server for generating gene set networks based on biclusters obtained by maximal frequent itemset mining.

Authors:  Kei-ichiro Takahashi; Ichigaku Takigawa; Hiroshi Mamitsuka
Journal:  PLoS One       Date:  2013-12-30       Impact factor: 3.240

7.  A survey of visualization tools for biological network analysis.

Authors:  Georgios A Pavlopoulos; Anna-Lynn Wegener; Reinhard Schneider
Journal:  BioData Min       Date:  2008-11-28       Impact factor: 2.522

8.  A visual analytics approach for understanding biclustering results from microarray data.

Authors:  Rodrigo Santamaría; Roberto Therón; Luis Quintales
Journal:  BMC Bioinformatics       Date:  2008-05-27       Impact factor: 3.169

Review 9.  Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

Authors:  Georgios A Pavlopoulos; Dimitris Malliarakis; Nikolas Papanikolaou; Theodosis Theodosiou; Anton J Enright; Ioannis Iliopoulos
Journal:  Gigascience       Date:  2015-08-25       Impact factor: 6.524

10.  BicOverlapper 2.0: visual analysis for gene expression.

Authors:  Rodrigo Santamaría; Roberto Therón; Luis Quintales
Journal:  Bioinformatics       Date:  2014-03-03       Impact factor: 6.937
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