PGMRA: a web server for (phenotype × genotype) many-to-many relation analysis in GWAS Arnedo Fernández, Francisco Javier Val Muñoz, María Coral Del Erausquin, Gabriel Alejandro de Romero-Zaliz, Rocío Swrakic, Dragan Cloninger, Claude Robert Zwir Nawrocki, Jorge Sergio Igor Single nucleotide polymorphisms (SNPs) Genome-wide association studies (GWAS) Phenotype Genotype Regulatory network Schizophrenia Disease It has been proposed that single nucleotide polymorphisms (SNPs) discovered by genome-wide association studies (GWAS) account for only a small fraction of the genetic variation of complex traits in human population. The remaining unexplained variance or missing heritability is thought to be due to marginal effects of many loci with small effects and has eluded attempts to identify its sources. Combination of different studies appears to resolve in part this problem. However, neither individual GWAS nor meta-analytic combinations thereof are helpful for disclosing which genetic variants contribute to explain a particular phenotype. Here, we propose that most of the missing heritability is latent in the GWAS data, which conceals intermediate phenotypes. To uncover such latent information, we propose the PGMRA server that introduces phenomics—the full set of phenotype features of an individual—to identify SNP-set structures in a broader sense, i.e. causally cohesive genotype–phenotype relations. These relations are agnostically identified (without considering disease status of the subjects) and organized in an interpretable fashion. Then, by incorporating a posteriori the subject status within each relation, we can establish the risk surface of a disease in an unbiased mode. This approach complements—instead of replaces—current analysis methods. The server is publically available at http://phop.ugr.es/fenogeno. 2013-10-18T08:16:20Z 2013-10-18T08:16:20Z 2013 journal article Arnedo, J.; et al. PGMRA: a web server for (phenotype × genotype) many-to-many relation analysis in GWAS. Nucleic Acids Research, 41(W1): W142-W149 (2013). [http://hdl.handle.net/10481/28445] 0305-1048 1362-4962 http://hdl.handle.net/10481/28445 10.1093/nar/gkt496 eng open access Oxford University Press (OUP)