Methods

eQTL profiles mapped in the original papers are used for visualization and investigation, except for those found in Lowry et al. 2013 which were re-mapped from the original genotypes and gene expression data by a single marker model using a linear model in R.

Correlation

All pairwise correlations between eQTL patterns were calculated using the Pearson correlation coefficients between the eQTL patterns of genes within an experiment using the R function ‘cor’, on the LOD scores.

Mapping

The markers are mapped according to the original publications. The physical positions of the markers were used to compare and integrate the genetic maps of the different populations and can be obtained from the WormQTL 2 homepage.

LOD score threshold

The LOD score thresholds are taken from the corresponding papers. Original determined genome-wide threshold levels may be applied to call significant eQTLs. The thresholds for comparing eQTLs will vary depending on the number of genes, eQTLs and populations involved.

Software

WormQTL 2 was implemented in the Python Django web framework using a MySQL database backend. The web pages include Javascript, using JQuery, and the d3 and bootstrip libraries. The cis/trans plot and QTL profile plots built upon work by Karl Broman (Broman, 2015).

Getting started

To view all eQTL profiles for a certain gene, type its name or ID in the text box and click the Search button.

To see a cis-trans plot with all eQTL peaks for a certain experiment, click on the experiment name.

You can search with a keyword to find genes and gene ontology (GO) categories.

Select the examples menu to see some example analysis with WormQTL 2.

Find correlating eQTL profiles

Show all genes for which the eQTL profile correlates with that of the query gene above the set cut-off, in the selected experiment.

Strongly correlating eQTL profiles could indicate that the genes are regulated by the same loci.

Query per locus

Show the eQTL profiles of genes with a LOD score above the threshold at the selected locus in the selected experiment.

A locus can be a marker, a gene name, gene id or a genomic position (i.e. 2:11095452).

What is WormQTL 2?

WormQTL 2 is the C.elgans workbench and database for eQTL analysis.

It allows easy access to the data of all published Caenorhabditis elegans genetical genomics experiments.

WormQLT2 was modelled after AraQTL (the arabidopsis eQTL resource).

A paper describing WormQTL2 was published in Database:
WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

What is an eQTL?

An eQTL is a genetic locus that was shown to affect the expression of the current gene.

eQTLs are the result of combining genomics with genetics, in "genetical genomics" Jansen and Nap Trends in Genetics 17(7):388-91 (2001)