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PARIS specifications


Unique identifier OMICS_11440
Alternative name Pathway Analysis by Randomization Incorporating Structure
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Database management system SQLite
Computer skills Advanced
Version 1.1.3
Stability Stable
Maintained Yes


No version available



  • person_outline Jessica Cooke Bailey

Publications for Pathway Analysis by Randomization Incorporating Structure

PARIS citations


Shared Genetic Etiology of Autoimmune Diseases in Patients from a Biorepository Linked to De identified Electronic Health Records

Front Genet
PMCID: 5071319
PMID: 27812365
DOI: 10.3389/fgene.2016.00185
call_split See protocol

[…] (O'Reilly et al., ) in R software version 3.2.3 (R Development Core Team, ). Twenty-two SNPs from the MultiPhen joint model (i.e., MS, CD, and RA) with a p < 0.05 were further characterized using the Pathway Analysis by Randomization incorporating Structure (PARIS), a SNP-based pathway analysis tool that identifies biological pathways significantly enriched by genetic variants adjusted for linkage […]


Assessing the Association of Mitochondrial Genetic Variation With Primary Open Angle Glaucoma Using Gene Set Analyses

PMCID: 5040191
PMID: 27661856
DOI: 10.1167/iovs.16-20017

[…] mitochondrial proteome because the platform used for genotyping does not include a sufficient number of mitochondrial DNA variants for analysis using pathway software programs, including the program Pathway Analysis by Randomization Incorporating Structure (PARIS;, in the public domain) used for this study. We identified 1010 nuclear-encoded mito […]


Genetic Association Analysis of Drusen Progression

PMCID: 4849854
PMID: 27116550
DOI: 10.1167/iovs.15-18571

[…] against the genome-wide SNP data present on the exome-chip array. A minor allele frequency cutoff of 0.05 was used. Pathway analysis was performed on the results of the single variant tests using the pathway analysis by randomization incorporating structure (PARIS) algorithm, and restricted to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, which contains 199 defined pathways. […]


Estimating cumulative pathway effects on risk for age related macular degeneration using mixed linear models

BMC Bioinformatics
PMCID: 4606903
PMID: 26467978
DOI: 10.1186/s12859-015-0760-4

[…] Encyclopedia of Genes and Genomes (KEGG) [], or Reactome []. These methods then utilize analytical approaches, such as Gene Relationships Across Implicated Loci (GRAIL), Gene Set Analysis (GSA), and Pathway Analysis by Randomization Incorporating Structure (PARIS), to determine the significance of pathways, usually using gene or SNP p-values or genotype data to calculate a rank-based pathway stat […]


Loci nominally associated with autism from genome wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci

Mol Autism
PMCID: 3484025
PMID: 22591576
DOI: 10.1186/2040-2392-3-3

[…] m GWAS have recently been published, showing enrichment of sub-genome-wide significant associations with pathways of prior interest in autism. For example, Yaspan and colleagues applied their method (pathway analysis by randomization incorporating structure) to the available Autism Genetic Resource Exchange GWAS dataset, subsequently identifying over-representation of pathways involved in ubiquiti […]


Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma

PLoS Genet
PMCID: 3343074
PMID: 22570617
DOI: 10.1371/journal.pgen.1002654

[…] Pathway analysis was done using the Pathway Analysis by Randomization Incorporating Structure (PARIS) pathway analysis software package . Genes comprising the transforming growth factor beta (TGF-beta) pathway were identified using the […]


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PARIS institution(s)
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA; Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Biomedical and Translational Informatics Program, Geisinger Health System, Danville, PA, USA; Department of Human Genetics, Genentech, Inc, South San Francisco, CA, USA
PARIS funding source(s)
This work was supported by EY012118 and AG047133. The NEIGHBORHOOD is supported by National Institutes of Health/NEI (1R01EY022305) and by the Center for Inherited Disease Research (genotyping).

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