Skip Navigation



Bioinformatics Advance Access published online on July 14, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti574
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
21/17/3575    most recent
bti574v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Wrobel, G.
Right arrow Articles by Primig, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wrobel, G.
Right arrow Articles by Primig, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 17, 2005
Revised May 9, 2005
Accepted July 5, 2005

Applications note

goCluster integrates statistical analysis and functional interpretation of microarray expression data

Gunnar Wrobel 1, Frédéric Chalmel 1, and Michael Primig 1*

1 Biozentrum & Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland

* To whom correspondence should be addressed.
Michael Primig, E-mail: michael.primig{at}unibas.ch


  Abstract

Motivation: Several tools that facilitate the interpretation of transcriptional profiles using gene annotation data are available but most of them combine a particular statistical analysis strategy with functional information. goCluster extends this concept by providing a modular framework that facilitates integration of statistical and functional microarray data analysis and interpretation.

Results: goCluster enables scientists to employ annotation information, clustering algorithms and visualization tools in their array data analysis and interpretation strategy. The package provides four clustering algorithms and GeneOntology terms as proto-type annotation data. The functional analysis is based on the hypergeometric distribution whereby the Bonferroni correction or the false discovery rate (FDR) can be used to correct for multiple testing. The approach implemented in goCluster was successfully applied to interpret the results of complex mammalian and yeast expression data obtained with high density oligonucleotide microarrays (GeneChips).

Availability: goCluster is available via the BioConductor portal at www.bioconductor.org. The software package, detailed documentation, user- and developer guides as well as other background information are also accessible via a web portal at http://www.bioz.unibas.ch/gocluster.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
D. W. Huang, B. T. Sherman, and R. A. Lempicki
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
Nucleic Acids Res., January 1, 2009; 37(1): 1 - 13.
[Abstract] [Full Text] [PDF]

Home page
 Journals of Gerontology Series A: Biological Sciences and Medical SciencesHome page
G. Yiu, A. McCord, A. Wise, R. Jindal, J. Hardee, A. Kuo, M. Y. Shimogawa, L. Cahoon, M. Wu, J. Kloke, et al.
Pathways Change in Expression During Replicative Aging in Saccharomyces cerevisiae
J. Gerontol. A Biol. Sci. Med. Sci., January 1, 2008; 63(1): 21 - 34.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. F. Schwarz, O. Hadicke, J. Erdmann, A. Ziegler, D. Bayer, and S. Moller
SNPtoGO: characterizing SNPs by enriched GO terms
Bioinformatics, January 1, 2008; 24(1): 146 - 148.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Van Vooren, B. Thienpont, B. Menten, F. Speleman, B. D. Moor, J. Vermeesch, and Y. Moreau
Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations
Nucleic Acids Res., April 3, 2007; 35(8): 2533 - 2543.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.