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

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/.

authors

• Rusyn, Ivan

published proceedings

• Bioinformatics

author list (cited authors)

• Gatti, D. M., Sypa, M., Rusyn, I., Wright, F. A., & Barry, W. T.

citation count

• 5

complete list of authors

• Gatti, Daniel M||Sypa, Myroslav||Rusyn, Ivan||Wright, Fred A||Barry, William T

publication date

• February 2009

publisher

• Oxford University Press (OUP)  Publisher

published in

• Bioinformatics  Journal

keywords

• Algorithms
• Computational Biology
• Computer Graphics
• Gene Expression Profiling
• Oligonucleotide Array Sequence Analysis
• Software
• User-Computer Interface

PubMed Central ID

• 19098030

Digital Object Identifier (DOI)

• 10.1093/bioinformatics/btn655

start page

• 541

end page

• 542

volume

• 25

issue

• 4

URL

• http://dx.doi.org/10.1093/bioinformatics/btn655