Multiple testing in large-scale contingency tables: inferring patterns of pair-wise amino acid association in β-sheets

Authors:
Seoung Bum Kim;Kwok-Leung Tsui;Mark Borodovsky
Affiliations:
Department of Industrial and Manufacturing Systems Engineering, University of Texas at Arlington, P.O. Box 19017, Arlington, TX 76019, USA.;School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.;School of Biology and Wallace H. Coulter Department of Biomedical Engineering, Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2006

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Abstract

This study examines the feasibility of using multiple testingprocedures for an inference of independence of categories in eachcell in contingency tables. In the simulation study, we compare theperformance of various multiple testing procedures in a contingencytable setup and demonstrate the relationship among the proportionof true null hypothesis, type I error, power, and false discoveryrate. Finally, we apply the proposed methodology to identify thepatterns of pair-wise associations of amino acids involved inβ-sheet bridges in proteins. We identify a number of aminoacid pairs that exhibit either strong or weak association.