Skip Navigation



Bioinformatics Advance Access published online on February 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth087
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
20/9/1462    most recent
bth087v1
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
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Cheng, J.
Right arrow Articles by Siani-Rose, M. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Cheng, J.
Right arrow Articles by Siani-Rose, M. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received July 10, 2003
Revised October 29, 2003
Accepted December 22, 2003

Applications note

NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis

Jill Cheng 1*, Shaw Sun 1, Adam Tracy 1, Earl Hubbell 1, Joseph Morris 1, Venu Valmeekam 1, Andrew Kimbrough 1, Melissa S. Cline 1, Guoying Liu 1, Ron Shigeta 1, David Kulp 1, Michael A. Siani-Rose 1

1 Affymetrix Corporation, Bioinformatics, 6550 Vallejo Street, Suite 100, Emeryville, CA 94608, USA

* To whom correspondence should be addressed. E-mail: jill_cheng{at}affymetrix.com.


  Abstract

Summary: The NetAffx Gene Ontology (GO) Mining Tool is a web-based, interactive tool which permits traversal of the GO graph in the context of microarray data. It accepts a list of Affymetrix probe sets and renders a GO graph as a heat map colored according to significance measurements. The rendered graph is interactive, with nodes linked to public web sites, and to lists of the relevant probe sets. The GO Mining Tool provides visualization combining biological annotation with expression data, encompassing thousands of genes in one interactive view.

Availability: Go Mining Tool is freely available at http://www.affymetrix.com/analysis/query/go_analysis.affx.


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
 Cancer Res.Home page
J. C. Nwachukwu, P. Mita, R. Ruoff, S. Ha, Q. Wang, S. J. Huang, S. S. Taneja, M. Brown, W. L. Gerald, M. J. Garabedian, et al.
Genome-Wide Impact of Androgen Receptor Trapped clone-27 Loss on Androgen-Regulated Transcription in Prostate Cancer Cells
Cancer Res., April 1, 2009; 69(7): 3140 - 3147.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Frijters, B. Heupers, P. van Beek, M. Bouwhuis, R. van Schaik, J. de Vlieg, J. Polman, and W. Alkema
CoPub: a literature-based keyword enrichment tool for microarray data analysis
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W406 - W410.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Q. Zheng and X.-J. Wang
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W358 - W363.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
M. T. Flowers, M. P. Keller, Y. Choi, H. Lan, C. Kendziorski, J. M. Ntambi, and A. D. Attie
Liver gene expression analysis reveals endoplasmic reticulum stress and metabolic dysfunction in SCD1-deficient mice fed a very low-fat diet
Physiol Genomics, May 1, 2008; 33(3): 361 - 372.
[Abstract] [Full Text] [PDF]

Home page
 J. Leukoc. Biol.Home page
M. W. Wlodarski, Z. Nearman, A. Jankowska, N. Babel, J. Powers, P. Leahy, H.-D. Volk, and J. P. Maciejewski
Phenotypic differences between healthy effector CTL and leukemic LGL cells support the notion of antigen-triggered clonal transformation in T-LGL leukemia
J. Leukoc. Biol., March 1, 2008; 83(3): 589 - 601.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. Nettleton, J. Recknor, and J. M. Reecy
Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis
Bioinformatics, January 15, 2008; 24(2): 192 - 201.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Goffard and G. Weiller
PathExpress: a web-based tool to identify relevant pathways in gene expression data
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W176 - W181.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
I. Rivals, L. Personnaz, L. Taing, and M.-C. Potier
Enrichment or depletion of a GO category within a class of genes: which test?
Bioinformatics, February 15, 2007; 23(4): 401 - 407.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Physiol. Cell Physiol.Home page
D. Kuninger, A. Wright, and P. Rotwein
Muscle cell survival mediated by the transcriptional coactivators p300 and PCAF displays different requirements for acetyltransferase activity
Am J Physiol Cell Physiol, October 1, 2006; 291(4): C699 - C709.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Wu, X. Mao, T. Cai, J. Luo, and L. Wei
KOBAS server: a web-based platform for automated annotation and pathway identification.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W720 - W724.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. S. Huo, R. C. McEachin, T. X. Cui, N. K. Duggal, T. Hai, D. J. States, and J. Schwartz
Profiles of Growth Hormone (GH)-regulated Genes Reveal Time-dependent Responses and Identify a Mechanism for Regulation of Activating Transcription Factor 3 By GH
J. Biol. Chem., February 17, 2006; 281(7): 4132 - 4141.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X. Mao, T. Cai, J. G. Olyarchuk, and L. Wei
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary
Bioinformatics, October 1, 2005; 21(19): 3787 - 3793.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. Yu, W. Sun, S. Yuan, and K.-C. Li
Study of coordinative gene expression at the biological process level
Bioinformatics, September 15, 2005; 21(18): 3651 - 3657.
[Abstract] [Full Text] [PDF]

Home page
 Toxicol SciHome page
R. A. Currie, V. Bombail, J. D. Oliver, D. J. Moore, F. L. Lim, V. Gwilliam, I. Kimber, K. Chipman, J. G. Moggs, and G. Orphanides
Gene Ontology Mapping as an Unbiased Method for Identifying Molecular Pathways and Processes Affected by Toxicant Exposure: Application to Acute Effects Caused by the Rodent Non-Genotoxic Carcinogen Diethylhexylphthalate
Toxicol. Sci., August 1, 2005; 86(2): 453 - 469.
[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.