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Updated: May 4, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

ALEA: a toolbox for allele-specific epigenomics analysis.

Hamid Younesy¹, Torsten Möller¹, Alireza Heravi-Moussavi²

¹Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.

Bioinformatics (Oxford, England)

|December 28, 2013

Summary

This summary is machine-generated.

ALEA is a new computational toolbox for allele-specific epigenomics analysis. It identifies associations between epigenetic modifications and specific allelic variants in human and mouse cells using next-generation sequencing data.

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Area of Science:

Genomics
Computational Biology
Epigenetics

Background:

Assessing gene expression and epigenomic status via sequencing methods offers opportunities to link allelic differences with epigenomic status.
Allele-specific epigenomics analysis is crucial for understanding genotype-phenotype relationships.

Purpose of the Study:

To present ALEA, a computational toolbox for allele-specific epigenomics analysis.
To enable the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells.

Main Methods:

ALEA is a customizable pipeline of command-line tools for analyzing next-generation sequencing data (ChIP-seq, RNA-seq).
It incorporates allelic variation data into existing resources.
The toolbox processes raw sequencing data to produce separate allelic tracks for genome browsers.

Main Results:

ALEA successfully performs allele-specific analysis of sequencing data.
The pipeline was validated using human and hybrid mouse ChIP-seq and RNA-seq data.
It facilitates the visualization of allele-specific epigenomic data.

Conclusions:

ALEA provides a robust computational framework for allele-specific epigenomics analysis.
This toolbox enhances the ability to correlate epigenetic modifications with specific allelic variants.
ALEA is a valuable resource for researchers studying the interplay between epigenetics and genetic variation.