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High-speed westfall-young permutation procedure for genome-wide association studies
2015
Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '15
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We introduce an algorithm to accelerate WY, named High-speed Westfall-Young permutation procedure (HWY). HWY utilizes three techniques to make WY computationally practical. ...
Genome-wide association studies (GWASs) are widely used to investigate statistically significant associations between diseases and single nucleotide polymorphisms (SNPs) to identify causal factors of diseases ...
Shuji Suzuki for insightful discussions and suggestions. Supercomputing resources were provided by NIG (ROIS). AT is supported by JSPS Research Fellowships for Young Scientists. ...
doi:10.1145/2808719.2808721
dblp:conf/bcb/TeradaKS15
fatcat:djplvyw6wravjmfc5dtu5z3sfu
PERMORY-MPI: a program for high-speed parallel permutation testing in genome-wide association studies
2012
Bioinformatics
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PERMORY is software for accelerated permutation testing of genome-wide association studies (GWAS). ...
ACKNOWLEDGEMENT We thank the reviewers for their valuable comments. ...
In particular, the genome-wide adjusted P-value for marker j is calculated using a single step max-t procedure (Westfall and Young, 1993) . Assuming a set of, say, r permutations, k = 1,... ...
doi:10.1093/bioinformatics/bts086
pmid:22345620
fatcat:oajmctcnefcr3osnkyuafk4zoq
On permutation procedures for strong control in multiple testing with gene expression data
2013
Statistics and its Interface
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We consider two popular, permutation-based, step-down procedures of p-values adjustment in multiple testing problems known as min P and max T and intended for strong control of the family-wise error rate ...
We first modify these subvectors into { X i , i ∈ M } and { Y i , i ∈ M } by replacing for i ∈ M \M 0 the corresponding components with the mutually independent, standard Gaussian variables independent ...
Westfall and Young (1993) proposed two permutation based procedures, min P and max T , designed to control the family-wise error rate without modeling the dependence among the individual tests. ...
doi:10.4310/sii.2013.v6.n1.a8
pmid:24376905
pmcid:PMC3873102
fatcat:xb7dqlvypbayjadzp2u3iwqpiy
Multiple hypothesis testing in genomics
2014
Statistics in Medicine
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It arises when a single researcher simultaneously tests many genomic markers or probes. It arises when these probes are tested for association with multiple phenotypes of interest. ...
As the type I errors among the findings are likely to be the most surprising and novel ones, they have a high risk of finding their way into publications. ...
In genome-wide association studies, for example, it has been asserted that the correlation structure between the p-values in such a study is such that a fixed genome-wide significance level of α = 5 × ...
doi:10.1002/sim.6082
pmid:24399688
fatcat:jfi6qcguyzazvdztnaby7dzv4q
Network-guided search for genetic heterogeneity between gene pairs
2020
Bioinformatics
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Additionally, we find novel associations for multiple A. thaliana phenotypes, and for a study of rare variants in migraine patients. ...
Results We propose a novel method SiNIMin that addresses these two aspects by finding pairs of interacting genes that are, upon combination, associated with a phenotype of interest under a model of genetic ...
Given a sufficient number of permutations n p , the FWER at a significance threshold d can be estimated as 2.3.3 Westfall-Young permutations for FWER control One disadvantage of Tarone's procedure is its ...
doi:10.1093/bioinformatics/btaa581
pmid:32573681
pmcid:PMC8034561
fatcat:vvfsa3uoefbnpem7boylimgaeq
Significance analysis of functional categories in gene expression studies: a structured permutation approach
2005
Bioinformatics
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Motivation: In high-throughput genomic and proteomic experiments, investigators monitor expression across a set of experimental conditions. ...
SAFE is a two-stage, permutation-based method that can be applied to various experimental designs, accounts for the unknown correlation among genes and enables permutation-based estimation of error rates ...
ACKNOWLEDGEMENTS We thank the reviewers for their helpful suggestions. Karl Strohmaier provided assistance with Perl scripts to incorporate the GO inheritance structure. ...
doi:10.1093/bioinformatics/bti260
pmid:15647293
fatcat:7mroc4dw4ncgraujphnyx7d2oe
Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays
2003
Bioinformatics
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Motivation: In microarray studies gene discovery based on fold-change values is often misleading because error variability for each gene is heterogeneous under different biological conditions and intensity ...
Several statistical testing methods for differential gene expression have been suggested, but some of these approaches are underpowered and result in high false positive rates because within-gene variance ...
ACKNOWLEDGEMENTS We greatly thank for the reviewers' and the associate editor's comments, which helped us to improve our manuscript significantly. ...
doi:10.1093/bioinformatics/btg264
pmid:14555628
fatcat:z77kwgyp55gr7b6zekucjiqncq
Resampling-based multiple testing for microarray data analysis
2003
Test (Madrid)
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In their 1993 book, Westfall & Young propose resampling-based p-value adjustment procedures which are highly relevant to microarray experiments. ...
Adjusted p-values for different approaches are applied to gene expression data from two recently published microarray studies. The properties of these procedures for multiple testing are compared. ...
Acknowledgments We thank Greg Grant, John Storey and Peter Westfall for their helpful discussions on the subject matter of this paper. ...
doi:10.1007/bf02595811
fatcat:m7ke557yybb55fx42lvfpp7w54
Genome-wide detection of intervals of genetic heterogeneity associated with complex traits
2015
Bioinformatics
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We demonstrate on Arabidopsis thaliana genome-wide association study data that our approach can discover regions that exhibit genetic heterogeneity and would be missed by single-locus mapping. ...
that is to be tested for genetic heterogeneity, potentially missing intervals of high relevance, or (ii) they suffer from an enormous multiple hypothesis testing problem due to the large number of potential ...
An alternative to the lack of power of the Bonferroni correction is to use permutation-testing methods, such as the Westfall-Young (WY) permutation testing procedure (Westfall and Young, 1993) , to empirically ...
doi:10.1093/bioinformatics/btv263
pmid:26072488
pmcid:PMC4559912
fatcat:npe55gj6wza2hfy3ubjouim76a
TEAM: efficient two-locus epistasis tests in human genome-wide association study
2010
Bioinformatics
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As a promising tool for identifying genetic markers underlying phenotypic differences, genome-wide association study (GWAS) has been extensively investigated in recent years. ...
In this article, we propose an efficient algorithm, TEAM, which significantly speeds up epistasis detection for human GWAS. ...
Then, we present the findings of epistasis detection in simulated human genome-wide study. ...
doi:10.1093/bioinformatics/btq186
pmid:20529910
pmcid:PMC2881371
fatcat:4yztk3hlmrayjhrlgspjok6eg4
Multiple Hypothesis Testing in Microarray Experiments
2003
Statistical Science
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The biological question of differential expression can be restated as a problem in multiple hypothesis testing: the simultaneous test for each gene of the null hypothesis of no association between the ...
., genes whose expression levels are associated with a response or covariate of interest. ...
Microarrays are being applied increasingly in biological and medical research to address a wide range of problems, such as the classification of tumors or the study of host genomic responses to bacterial ...
doi:10.1214/ss/1056397487
fatcat:qu7qoag6dffevhbsazdg74haba
Assessing Differential Expression in Two-Color Microarrays: A Resampling-Based Empirical Bayes Approach
2013
PLoS ONE
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Microarrays are widely used for examining differential gene expression, identifying single nucleotide polymorphisms, and detecting methylation loci. ...
The Significance Analysis of Microarrays, another widely used microarray data analysis method, is based on a permutation test and is robust to non-normally distributed data; however, the Significance Analysis ...
Acknowledgments Many thanks to the reviewers for their thorough review and insightful comments which helped us improved this manuscript.
Author Contributions ...
doi:10.1371/journal.pone.0080099
pmid:24312198
pmcid:PMC3842292
fatcat:3fjl62p3jfgp5ppx7m2awufrlu
Practical aspects of genome-wide association interaction analysis
2014
Human Genetics
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Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK) and our colleagues François Van Lishout, Jestinah ...
Department of Neuroscience, Jacksonville, FL, USA; Mayo Clinic Florida, Department of Neurology, Jacksonville, FL, USA), Denise Harold and Julie Williams (GERAD1 Consortium; Medical Research Council Centre for ...
assessments (maxT method) (Westfall and Young 1993a), etc.]. ...
doi:10.1007/s00439-014-1480-y
pmid:25164382
fatcat:zue2ifjuhjdm5dk4bp7rhbqi5y
Efficient Algorithms for Detecting Genetic Interactions in Genome-Wide Association Study
2012
Proceedings of the 18th ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '12
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Xiang Zhang: Efficient Algorithms for Detecting Genetic Interactions in Genome-Wide Association Study. (Under the direction of Wei Wang.) ...
Genome-wide association study (GWAS) aims to find genetic factors underlying complex phenotypic traits, for which epistasis or gene-gene interaction detection is often preferred over a single-locus approach ...
Our FastChi algorithm makes permutation procedure more feasible in genome-wide association mapping. ...
doi:10.1145/2339530.2378375
fatcat:zvlmyxim6zgfnfd7l7syzrnrr4
EzArray: A web-based highly automated Affymetrix expression array data management and analysis system
2008
BMC Bioinformatics
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With accumulating microarray data deposited in public databases, easy-to-use programs to re-analyze previously published microarray data are in high demand. ...
Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. ...
We would like to thank Emily Powell for the critical review the manuscript. ...
doi:10.1186/1471-2105-9-46
pmid:18218103
pmcid:PMC2265266
fatcat:qalzwdqtsbgahhxt4jhborcqse
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