QTLNetMiner – a Modern Web Application for Network Based Gene-Phenotype Discovery

Discovering those genes and biological processes that are involved in the expression of complex traits in crops, animals or humans is a challenging task for many geneticists and biologists. QTLNetMiner is a web application that efficiently interrogates large genome-scale knowledge networks (built using the free and open-source data integration software www.ondex.org) with user data such as search terms, QTL and gene list. The data visualisation components have been developed specifically for facilitating candidate gene prioritization and gene-phenotype discovery. The main key benefits of QTLNetMiner are: i) the user is guided and supported when writing the search terms through features such as real-time user feedback and query term suggestions; ii) the output is dynamic and rich in detail including different visualisations such as tables, networks and genome coordinate-based maps that are easy to navigate through a tabbed interface, and with extensive cross-referencing; iii) a lightweight JavaScript-based network viewer, called KNETviewer, that is optimised for visualising and exploring data rich knowledge networks and incorporates search-specific visualisation effects; iv) the underlying knowledge networks are regularly updated to include the latest database releases and v) the software platform is configurable and portable so that developers can easily build instances for new species. We have developed genome-scale knowledge networks and QTLNetMiner instances for various plant and animal species: https://ondex.rothamsted.ac.uk/QTLNetMiner/.