eQTL Explorer

Category Genomics>Genetic Data Analysis/Tools

Abstract eQTL Explorer is an expression Quantitative Trait Loci (eQTL) visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments.

eQTL Explorer stores gene expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface.

eQTL Explorer provides a new and advanced tool to interrogate these very large and complex datasets.

eQTL Explorer complements already available tools such as WebQTL (see G6G Abstract Number 20326) or QTL Express (recently replaced by GridQTL), but provides further capabilities by focusing on the visualization of 'genetic mapping' results and their integration with external information sources.

eQTL Explorer is unique in that it allows eQTL results across the whole genome from multiple array experiments to be displayed alongside (patho) physiological QTLs (pQTLs) mapped to the genome.

eQTL Explorer Implementation and Visualization –

The application was designed to interrogate linkage analysis results carried out with QTL reaper, the batch-oriented version of WebQTL, for a study carried out in the BXH/HXB panel of recombinant inbred rat strains using the Affymetrix microarray platform.

However, it is generically applicable to any similar study.

Upon import into the database eQTLs are generated by amalgamating linkages of expression phenotypes to multiple tightly linked markers, using an algorithm described elsewhere.

The software also determines and indicates whether the eQTLs are cis- or trans-acting.

Exploration of the data starts with a ‘birds-eye’ view showing the distribution of eQTLs across the genome alongside the location of known physiological QTLs (pQTLs).

By default, eQTLs are plotted according to the location of the genetic marker at the peak of linkage and can be filtered according to whether they are cis- or trans-acting.

Displayed eQTLs can be filtered by level of significance by altering the P- value.

Less stringent P-values result in many data points being plotted and putative master regulators of expression are readily identifiable as clusters of co-localized eQTLs.

eQTL Explorer Integration with External Data Sources –

Individual chromosomes can be displayed in a separate view, which provides options to browse, zoom, and export data for detailed analysis.

Upon mousing-over an eQTL or pQTL, information relating to its genetic markers or probe set is displayed as tool tip text.

A pop-up menu provides access to annotations and cross-references to external data sources including Ensembl, the Rat Genome Database and National Center for Biotechnology Information (NCBI) Entrez.

Advanced options include the ability to select or highlight eQTLs associated with particular probe sets. Users can filter the data to display only eQTLs that are located within pQTLs.

Information relating to the displayed eQTLs and database cross- references can be exported in tabular format.

The genome-wide QTL reaper results for a particular probe set including P-value, likelihood ratio statistics and additive coefficient can be viewed as an XY plot.

eQTL Explorer Recent Improvements --

1) Correctly handles multiple organisms and experiments.

2) Can filter eQTLs based on different statistics.

3) Software can handle different probe set array platforms.

4) Software can plot eQTLs for both micro-satellite and Single Nucleotide Polymorphism (SNP) markers.

5) More Export features. Can export a selected probe set list and eQTLs overlapping selected pQTLs.

6) More flexibility with external links by changing the properties file (requires advanced knowledge of database).

7) Improved security features.

8) Quick summary option.

System Requirements

Contact manufacturer.


Manufacturer Web Site eQTL Explorer

Price Contact manufacturer.

G6G Abstract Number 20325

G6G Manufacturer Number 101821