New tool: PhenoLink

27 Aug 2012

Sacha van Hijum

In the ongoing quest to understand the relationship between genotype and phenotype, being able to quickly prioritize and visualize potential links and relations has become a true survival skill for those who are taking on the very large and very noisy ~omics datasets to dig for well hidden treasures. To support these efforts, Jumamurat Bayjanov and colleagues (CMBI, Radboud University Nijmegen Medical Centre) have developed PhenoLink, a web-tool that effectively deals with high noise levels and imbalances in phenotype data.

PhenoLink can be used on a wide variety of ~omics data. Identified links are visualized, which facilitates prioritizing these links as well as finding relations between features and between phenotypes, and identifying outliers in phenotype data. The authors applied PhenoLink on a set of 42 Lactobacillus plantarum strains to identify relationships between the presence/absence of genes and phenotypes defined by sugar utilization and nitrogen-dioxide production. In addition to known relationships, PhenoLink generated novel gene-to-phenotype relations in a well-studied strain (L. plantarum WCFS1).

Bayjanov JR, Molenaar D, Tzeneva V, Siezen RJ, van Hijum SA
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
BMC Genomics 2012;13:170

By: Esther Thole