title: Pathway analysis by randomization incorporating structure-PARIS: an update.
abstract: 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-download
  
  
  
  jnc43@case.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
authors.forename: Mariusz
authors.initials: M
authors.lastname: Butkiewicz
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
authors.forename: Jessica N
authors.initials: JN
authors.lastname: Cooke Bailey
authors.affiliation: Biomedical and Translational Informatics Program, Geisinger Health System, Danville, PA, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Frase
authors.affiliation: Biomedical and Translational Informatics Program, Geisinger Health System, Danville, PA, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Dudek
authors.affiliation: Department of Human Genetics, Genentech, Inc, South San Francisco, CA, USA.
authors.forename: Brian L
authors.initials: BL
authors.lastname: Yaspan
authors.affiliation: Biomedical and Translational Informatics Program, Geisinger Health System, Danville, PA, USA.
authors.forename: Marylyn D
authors.initials: MD
authors.lastname: Ritchie
authors.affiliation: Biomedical and Translational Informatics Program, Geisinger Health System, Danville, PA, USA.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Pendergrass
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: Haines
mesh_terms: D016208:Databases, Factual; D055106:Genome-Wide Association Study; D023281:Genomics; D006801:Humans; D012984:Software