AraQTL

Download the AraQTL manual

AraQTL is a web-based workbench and database for expression quantitative trait loci (eQTL) investigation.
It’s aim is to support the Arabidopsis and plant genetics community to utilities eQTL data in their research.
Currently it holds publicly available data of all published Arabidopsis eQTL studies. At the moment 5 genome-wide eQTL-sets can be explored and compared. This data was obtained from multiple recombinant inbred line (RIL) populations, Ler X Cvi, Bay X Sha, Cvi x Col, Bur x Col and Tsu x Kas and collected from several different stages and plant parts, like seeds, seedlings, whole rosettes or specific leaves.

Cis/Trans Plot

To get a genome-wide overview of the distribution of eQTL Cis/Trans Plot is most frequently used (REFs). The position of the eQTL peak is plotted on the x-axis against the position the genes for which these eQTL peak were found. We provide a default eQTL peak significance threshold per experiment at FDR of 0.05 for quick visualisation and an option to manually adjust this threshold for further exploration. The diagonal line of points show the Cis-eQTLs whereas so called hotspots or transbands can be recognized as vertical lines of points. This Cis/Trans plot has been made interactive by being able to select different experiment by a drop-down menu. Moreover the individual peaks (points in the Cis/Trans Plot) can be clicked to show the complete eQTL profile of the selected gene/peak. Lastly, the peak frequency per marker is show in the barplot below the Cis/Trans plot. Individual bars/markers can be clicked to obtain a figure and list with genes sharing a peak on the selected marker.

Gene eQTL profiles

In the “Gene eQTL profiles” window gene specific eQTL patterns between experiments can be compared. In this way experiment specific and co-occurring eQTLs can be easily recognised. Genes can be search and selected by a search box. The figure is interactive as points on the profile can be clicked which opens the window showing genes with an eQTL at the clicked marker in the selected experiment.

Gene interaction network for a single target gene

By selecting the eQTL interval on Gene eQTL profiles window, a gene interaction network can be constructed to show candidate regulatory genes. The network consist of nodes representing the target (blue) and candidate genes (orange, red, or green). The edges in the network show the interaction between genes based on a diverse sources of interactions, including gene annotation (from Gene Ontology), protein-protein interaction (from AraNet V2 and STRING), and transcription factor information (from PlantRegMap and AGRIS). The user can modify the network (e.g., filter out low-scored interaction and/or remove some sources of interactions) using the panel on the left.

Shared peaks

To find genes with an eQTL at the same locus the “Shared peaks” window can be used. The profile of the ten genes with the highest LOD score is show in the figure and a list with all genes with a peak above the threshold is place below the figure. Experiment, marker and threshold can be selected.

Gene interaction network for eQTL hotspot

A gene interaction network can be constructed from “Shared peaks” window by selecting the peak/eQTL hotspot. Genes with an eQTL on the hotspot (will be referred to as target genes) and genes located on the hotspot (will be referred to as candidate genes) are used to create a network where the connections between all of these genes are shown based on different types of interaction. The candidate and target genes have different colors and are located in separated columns. Within each column, the genes are ordered based on the number of interactions, which helps prioritize the candidate regulatory genes for the eQTL hotspot.

Correlated eQTL profiles

Extending from co-location of eQTL peaks the “Correlating eQTL profiles” window can be used to find genes with a correlated eQTL profile. This shows genes highly likely controlled by the loci (genetic architecture). Experiment, gene and correlation threshold can be selected. Specific peaks in the figures can be clicked to find genes sharing eQTLs at the selected marker.