Skip Navigation


Bioinformatics Advance Access originally published online on January 12, 2005
Bioinformatics 2005 21(9):1943-1949; doi:10.1093/bioinformatics/bti260
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/9/1943    most recent
bti260v1
Right arrow Alert me when this article is cited
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 ISI Web of Science
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 arrow Search for citing articles in:
ISI Web of Science (30)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Barry, W. T.
Right arrow Articles by Wright, F. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Barry, W. T.
Right arrow Articles by Wright, F. A.
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{at}oupjournals.org

Significance analysis of functional categories in gene expression studies: a structured permutation approach

William T. Barry 1, Andrew B. Nobel 2 and Fred A. Wright 1,*

1Department of Biostatistics, University of North Carolina at Chapel Hill North Carolina 27599-7420, USA
2Department of Statistics, University of North Carolina at Chapel Hill North Carolina 27599-3260, USA

*To whom correspondence should be addressed.

Motivation: In high-throughput genomic and proteomic experiments, investigators monitor expression across a set of experimental conditions. To gain an understanding of broader biological phenomena, researchers have until recently been limited to post hoc analyses of significant gene lists.

Method: We describe a general framework, significance analysis of function and expression (SAFE), for conducting valid tests of gene categories ab initio. SAFE is a two-stage, permutation-based method that can be applied to various experimental designs, accounts for the unknown correlation among genes and enables permutation-based estimation of error rates.

Results: The utility and flexibility of SAFE is illustrated with a microarray dataset of human lung carcinomas and gene categories based on Gene Ontology and the Protein Family database. Significant gene categories were observed in comparisons of (1) tumor versus normal tissue, (2) multiple tumor subtypes and (3) survival times.

Availability: Code to implement SAFE in the statistical package R is available from the authors.

Contact: fwright{at}bios.unc.edu; wbarry{at}bios.unc.edu; nobel{at}email.unc.edu

Supplementary information: http://www.bios.unc.edu/~fwright/SAFE


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
 Toxicol PatholHome page
N. Wakamatsu, J. B. Collins, J. S. Parker, M. Tessema, N. P. Clayton, T.-V. T. Ton, H.-H. L. Hong, S. Belinsky, T. R. Devereux, R. C. Sills, et al.
Gene Expression Studies Demonstrate that the K-ras/Erk MAP Kinase Signal Transduction Pathway and Other Novel Pathways Contribute to the Pathogenesis of Cumene-induced Lung Tumors
Toxicol Pathol, July 1, 2008; 36(5): 743 - 752.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Prevention ResearchHome page
Z. H. Gumus, B. Du, A. Kacker, J. O. Boyle, J. M. Bocker, P. Mukherjee, K. Subbaramaiah, A. J. Dannenberg, and H. Weinstein
Effects of Tobacco Smoke on Gene Expression and Cellular Pathways in a Cellular Model of Oral Leukoplakia
Cancer Prevention Research, July 1, 2008; 1(2): 100 - 111.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
D. Nam and S.-Y. Kim
Gene-set approach for expression pattern analysis
Brief Bioinform, May 1, 2008; 9(3): 189 - 197.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Shriner, T. M. Baye, M. A. Padilla, S. Zhang, L. K. Vaughan, and A. E. Loraine
Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies
Nucleic Acids Res., March 27, 2008; 36(4): e26 - e26.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
W. Rodenburg, A. G. Heidema, J. M. A. Boer, I. M. J. Bovee-Oudenhoven, E. J. M. Feskens, E. C. M. Mariman, and J. Keijer
A framework to identify physiological responses in microarray-based gene expression studies: selection and interpretation of biologically relevant genes
Physiol Genomics, March 10, 2008; 33(1): 78 - 90.
[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
 CirculationHome page
J. Loscalzo
Association Studies in an Era of Too Much Information: Clinical Analysis of New Biomarker and Genetic Data
Circulation, October 23, 2007; 116(17): 1866 - 1870.
[Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Maglietta, A. Piepoli, D. Catalano, F. Licciulli, M. Carella, S. Liuni, G. Pesole, F. Perri, and N. Ancona
Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data
Bioinformatics, August 15, 2007; 23(16): 2063 - 2072.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. J. Chen, T. Lee, R. R. Delongchamp, T. Chen, and C.-A. Tsai
Significance analysis of groups of genes in expression profiling studies
Bioinformatics, August 15, 2007; 23(16): 2104 - 2112.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. Huang and T. W. S. Chow
Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer
Bioinformatics, June 15, 2007; 23(12): 1503 - 1510.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Liu, J. M. Hughes-Oliver, and J. A. Menius Jr
Domain-enhanced analysis of microarray data using GO annotations
Bioinformatics, May 15, 2007; 23(10): 1225 - 1234.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. J. Goeman and P. Buhlmann
Analyzing gene expression data in terms of gene sets: methodological issues
Bioinformatics, April 15, 2007; 23(8): 980 - 987.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
T. S. Mehta, S. O. Zakharkin, G. L. Gadbury, and D. B. Allison
Epistemological issues in omics and high-dimensional biology: give the people what they want
Physiol Genomics, December 13, 2006; 28(1): 24 - 32.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Pathol.Home page
M. R. Graham, K. Virtaneva, S. F. Porcella, D. J. Gardner, R. D. Long, D. M. Welty, W. T. Barry, C. A. Johnson, L. D. Parkins, F. A. Wright, et al.
Analysis of the Transcriptome of Group A Streptococcus in Mouse Soft Tissue Infection
Am. J. Pathol., September 1, 2006; 169(3): 927 - 942.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
D. Nettleton
A discussion of statistical methods for design and analysis of microarray experiments for plant scientists.
PLANT CELL, September 1, 2006; 18(9): 2112 - 2121.
[Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Scheer, F. Klawonn, R. Munch, A. Grote, K. Hiller, C. Choi, I. Koch, M. Schobert, E. Hartig, U. Klages, et al.
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W510 - W515.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
P. Che, S. Lall, D. Nettleton, and S. H. Howell
Gene Expression Programs during Shoot, Root, and Callus Development in Arabidopsis Tissue Culture
Plant Physiology, June 1, 2006; 141(2): 620 - 637.
[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.