Journal Article

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

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

in Bioinformatics

Volume 25, issue 4, pages 541-542
Published in print February 2009 | ISSN: 1367-4803
Published online December 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn655

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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@bios.unc.edu; dmgatti@email.unc.edu

Journal Article.  1223 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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