Pathway analysis by randomization incorporating structure—PARIS: an update

• DOI: 10.1093/bioinformatics/btw130
• Publication Date: 2016-03-09T01:38:23Z
• Authors: Mariusz Butkiewicz; Jessica N. Cooke ...; Alex Frase; Scott Dudek; Brian L. Yaspan; Marylyn D. Ritchie; Sarah A. Pendergrass; Jonathan L. Haines
• Keywords: Pathway Analysis; Resampling

Abstract Motivation: 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 study results. Pathway-based analyses highlight biological pathways associated with phenotypes. PARIS uses a unique permutation strategy evaluate genomic structure of interrogated pathways, through testing features, thus eliminating many over-testing concerns arising other approaches. Results: have updated incorporate expanded definitions incorporation new expert knowledge multiple database sources, customized user provided and improvements in flexibility functionality. Availability implementation: is freely available all users at https://ritchielab.psu.edu/software/paris-download. Contact: [e-mail] Supplementary information: data are Bioinformatics online.