Title: 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

Addresses: 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

Abstract: This study examines the feasibility of using multiple testing procedures for an inference of independence of categories in each cell in contingency tables. In the simulation study, we compare the performance of various multiple testing procedures in a contingency table setup and demonstrate the relationship among the proportion of true null hypothesis, type I error, power, and false discovery rate. Finally, we apply the proposed methodology to identify the patterns of pair-wise associations of amino acids involved in β-sheet bridges in proteins. We identify a number of amino acid pairs that exhibit either strong or weak association.

Keywords: β-strands; contingency tables; false discovery rate; multiple testing; beta strands; bioinformatics; pattern inference; pair-wise associations; amino acids; simulation; beta-sheet bridges; proteins; individual cells.

DOI: 10.1504/IJBRA.2006.009768

International Journal of Bioinformatics Research and Applications, 2006 Vol.2 No.2, pp.193 - 217

Published online: 09 May 2006 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article