PCAN: phenotype consensus analysis to support disease-gene association

Patrice Godard, Matthew Page
2016 BMC Bioinformatics  
Bridging genotype and phenotype is a fundamental biomedical challenge that underlies more effective target discovery and patient-tailored therapy. Approaches that can flexibly and intuitively, integrate known gene-phenotype associations in the context of molecular signaling networks are vital to effectively prioritize and biologically interpret genes underlying disease traits of interest. Results: We describe Phenotype Consensus Analysis (PCAN); a method to assess the consensus semantic
more » ... ty of phenotypes in a candidate gene's signaling neighborhood. We demonstrate that significant phenotype consensus (p < 0.05) is observable for~67% of 4,549 OMIM disease-gene associations, using a combination of high quality String interactions + Metabase pathways and use Joubert Syndrome to demonstrate the ease with which a significant result can be interrogated to highlight discriminatory traits linked to mechanistically related genes. Conclusions: We advocate phenotype consensus as an intuitive and versatile method to aid disease-gene association, which naturally lends itself to the mechanistic deconvolution of diverse phenotypes. We provide PCAN to the community as an R package (http://bioconductor.org/packages/PCAN/) to allow flexible configuration, extension and standalone use or integration to supplement existing gene prioritization workflows.
doi:10.1186/s12859-016-1401-2 pmid:27923364 pmcid:PMC5142268 fatcat:hbsqwuatlncvtiiq33ovjee6bm