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Bioinformatics Advance Access originally published online on December 19, 2008
Bioinformatics 2009 25(4):541-542; doi:10.1093/bioinformatics/btn655
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy

Daniel M. Gatti 1,*, Myroslav Sypa 1, Ivan Rusyn 1, Fred A. Wright 2 and William T. Barry 3

1Department of Environmental Sciences & Engineering, 2Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599 and 3Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27705, USA

*To whom correspondence should be addressed.


  Abstract

Summary: A large number of websites and applications perform significance testing for gene categories/pathways in microarray data. Many of these packages fail to account for expression correlation between transcripts, with a resultant inflation in Type I error. Array permutation and other resampling-based approaches have been proposed as solutions to this problem. SAFEGUI provides a user-friendly graphical interface for the assessment of categorical significance in microarray studies, while properly accounting for the effects of correlations among genes. SAFEGUI incorporates both permutation and more recently proposed bootstrap algorithms that are demonstrated to be more powerful in detecting differential expression across categories of genes.

Availability: http://cebc.unc.edu/software/

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

Associate Editor: David Rocke

Received on November 19, 2008; revised on November 19, 2008; accepted on December 16, 2008

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