eQTL Explorer


eQTLexplorer is an eqtl visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments.

Rat Genomics and Models 2007 tutorial

Access Information

Anyone can log in to eQTL Explorer to access the public data using a guest account (no password is required). Login details are:


Individual and private access requires registration as a user of the database. For more information contact Jon Mangion.


Launch eQTLexplorer here.

Userguide in html format or pdf

Please ensure that your firewall allows access to port 3306.

Requires Java 1.4.2, which can be downloaded here.

"In-House" installation instructions and Java source-code are available:
Installation Bundle zip, tgz.
Java Source is here.

This software is freely available under GNU Public Licence for non-commercial research.

Mueller M et al. (2006) eQTLexplorer: integrated mining of genetical genomics experiments. Bioinformatics, 22: 509-11
Hubner N et al. (2005) Integrated Transcriptional Profiling and Linkage Analysis for Identification of Genes Underlying Disease. Nat Genet, 37: 243-253.


eQTLexplorer will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type.

A detailed user manual can be found here (pdf).

For any other queries contact Jon Mangion.

Recent Improvements

• Correctly handles multiple organisms and experiments.
• Can filter eQTLs based on different statistics.
• Software can handle different probeset array platforms.
• Software can plot eQTLs for both microsatellite and SNP markers.
• More Export features. Can export a selected probeset list, eQTLs overlapping selected pQTLs.
• More flexibility with external links by changing properties file (requires advanced knowledge of database).
• Improved security features.
• Quick summary option.
• Many minor bugs fixed.