Pathway analysis by randomization incorporating structure-PARIS: an update.

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Butkiewicz M, Cooke Bailey JN, Frase A, Dudek S, Yaspan BL, Ritchie MD, Pendergrass SA, Haines JL,.

We present an update to the pathway enrichment analysis tool ‘Pathway Analysis by Randomization Incorporating Structure (PARIS)’ that determines aggregated association signals generated from genome-wide association study results. Pathway-based analyses highlight biological pathways associated with phenotypes. PARIS uses a unique permutation strategy to evaluate the genomic structure of interrogated pathways, through permutation testing of genomic features, thus eliminating many of the over-testing concerns arising with other pathway analysis approaches.We have updated PARIS to incorporate expanded pathway definitions through the incorporation of new expert knowledge from multiple database sources, through customized user provided pathways, and other improvements in user flexibility and functionality.PARIS is freely available to all users at https://ritchielab.psu.edu/software/paris-downloadjnc43@case.eduSupplementary data are available at Bioinformatics online.

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Will Bush

Will Bush

William S. Bush, Ph.D., is a human geneticist and bioinformatician, and Assistant Professor within the Cleveland Institute for Computational Biology and the Department of Population and Quantitative Health Sciences at Case Western Reserve University.