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Fig. 1 | BMC Bioinformatics

Fig. 1

From: qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)

Fig. 1

Overview of the Eucalyptus Genome Integrative Explorer (EucGenIE) and qtlXplorer architecture. a EucGenIE integrates data from various sources and makes it available for query and exploration via a set of centralized plugins, e.g. interactive visualisation tools within the Genome Integrative Explorer System (GenIE-Sys). The Plant Genome Integrative Explorer (http://PlantGenIE.org) domain serves as an umbrella site linking four species-specific subdomains including EucGenIE.org. The databases contain tables for genomic, expression and QTL data from various sources. The Gene Search tool queries data from the genome table, enabling the user to search the database using gene identifiers or free-text search terms to create gene lists. A user can subsequently select tools to explore expression and annotation data linked to the genes in the active gene list, or create cross-species gene lists using orthology inference methods to move between different PlantGenIE domains. In the example presented, 84 laccase-related Eucalyptus genes were identified using the free text search term ‘laccase’. This corresponds to 23 poplar, 19 spruce and 11 Arabidopsis orthologs. PlantGenIE has external links to different web resources such as PLAZA, TAIR and Phytozome, to enable further downstream, in-depth exploration of biological data. b qtlXplorer is the first population genomics tool for the exploration of systems genetics data, currently only implemented in EucGenIE.org. There are six different starting points (1–6) for querying and browsing the data on an interactive Circos plot updating in real-time. Starting points 3 and 4 can also include other component traits (e.g. metabolites and metabolite QTLs) and starting points 5 and 6 can also include eigentraits or eigenmetabolites with the corresponding eigenQTLs. Each starting point consists of a searchable and sortable table from where a user can select instances. Input to qtlXplorer can be new or existing gene lists from the Gene Search tool in EucGenIE. Gene lists can be exported for further exploration in EucGenIE

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