ARTP2 (Adaptive Rank Truncated Product - Version 2) is an R package of biological pathway association analysis or pathway meta-analysis for genome-wide association studies (GWAS). It also provides tools for gene-level association test as a special case. ARTP2 is an enhanced version of two previously released packages ARTP and AdaJoint.
This online application was developed to assist epidemiological researchers for testing the association between complex disease/trait outcome and predefined pathways when only SNP-level summary statistics from one or multiple GWAS were available. We provide reference panel data incorporated from the 1000 Genomes Project to facilitate the studies on various populations. We also support over 4,700 pathways predefined by the BROAD Institute.
If you publish results that use ARTP2, please cite:
Zhang H, Wheeler W, Hyland LP, Yang Y, Shi J, Chatterjee N, Yu K. A powerful procedure for pathway-based meta-analysis using summary statistics identifies multiple pathways associated with type II diabetes.
Yu K, Li Q, Bergen AW, Pfeiffer RM, Rosenberg PS, Caporaso N, Kraft P, Chatterjee N. (2009) Pathway analysis by adaptive combination of P-values. Genet Epidemiol 33(8): 700 - 709
Zhang H, Shi J, Liang F, Wheeler W, Stolzenberg-Solomon R, Yu K. (2014) A fast multilocus test with adaptive SNP selection for large-scale genetic association studies. European Journal of Human Genetics, 22, 696 - 702