What is PARIS?
Pathway Analysis by Randomization Incorporating Structure (PARIS) is a software tool for conducting pathway analysis independent of study design. It is written in C++ and utilizes an SQLite database and variations file (both included in download) for analysis.
Why use PARIS ?
PARIS conducts pathway analysis to aggregate signals from GWAS analysis. It groups the SNPs into linkage disequilibrium (LD) features and single SNPs in linkage equilibrium (LE) features. Those features are then grouped by pathways (using the KEGG database or other sources) drawn from data in the accompanying database and variations file. The significance of a pathway is determined by permutation testing. In each permutation, the features in a pathway are replaced by a randomly selected set of features of similar size. The total number of features with a significant p-value are compared with the number of significant features in the permuted pathway. This approach has the following benefits:
- It only require the results of the GWAS analysis. No manipulation of the original data is needed.
- It permutes the genome rather than the data and is, therefore, faster to run than methods that require affection status permutation.
- The permutation testing accounts for LD, gene size, pathway size and SNP coverage.
PARIS 1.1.3, released on January 5, 2015