(1) How to get going with qtlXplorer:
(2) How to explore traits, genes and modules in qtlXplorer:
(3) How to explore QTLs and eQTLs in qtlXplorer:
qtlXplorer is a tool for browsing systems genetics data.
qtlXplorer provides the user with six different starting points (different panels) for browsing and querying the available systems genetics data i.e. phenotypic traits, trait QTLs, genes, eQTLs, gene expression modules (module eigengenes; MEs) and ME QTLs. Each starting point consists of a searchable and sortable table from where a user can select various items to use as a basis to query the database. Each query will redirect the user to the relevant panel where the results can be exported as tabulated file, and from where a next query will be possible.
In a parallel view, the genomic positions of genes, eQTLs, trait QTLs and ME QTLs are displayed on-the-fly, on a Circos plot. A user can switch between instances of trait QTLs and/or eQTLs, by changing the selection in the table. Selecting a QTL of interest on the interactive Circos plot will open the JBrowse tool, making it possible to explore and browse the underlying genes.
After importing a gene list, a user can:
– get the eQTLs corresponding to the genes in the list,
– get QTLs that overlap (co-localize) with the genomic positions of the genes or
– filter to keep only genes with a high (user-provided cut-off) gene-gene correlation.
After selecting a set of eQTLs from the eQTL panel, a user can:
– save the target genes to a gene list (for further exploration within EucGenIE),
– get genes that underlie the query eQTLs or
– get eQTLs or trait QTLs that overlap (co-localize) with the genomic position of the query eQTLs.
Systems genetics data: (i) Trait QTLs from population-wide phenotype data; (ii) eQTLs from population-wide transcriptome data; (iii) co-expression modules from the transcriptome data resulting in module eigengenes (weighted summary profiles representing each module) and module eigengene QTLs.
qtlXplorer was developed in Java, using Google Web Toolkit. The web based front-end communicates with the database via PHP and data is sent in JSON format. The configuration file for the interactive Circos is created based on the selected items and then executed and linked to an imagemap file. This links the areas on the image to the JBrowse instance in EucGenIE.