title: ALEA: a toolbox for allele-specific epigenomics analysis.
abstract: The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data.
  
  
  
  The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea CONTACT: : mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: 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 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.
authors.forename: Hamid
authors.initials: H
authors.lastname: Younesy
authors.affiliation: 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 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.
authors.forename: Torsten
authors.initials: T
authors.lastname: Möller
authors.affiliation: 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.
authors.forename: Alireza
authors.initials: A
authors.lastname: Heravi-Moussavi
authors.affiliation: 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.
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Cheng
authors.affiliation: 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.
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Costello
authors.affiliation: 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.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Lorincz
authors.affiliation: 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 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.
authors.forename: Mohammad M
authors.initials: MM
authors.lastname: Karimi
authors.affiliation: 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.
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
mesh_terms: D000483:Alleles; D000818:Animals; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D057890:Epigenomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D051379:Mice; D012313:RNA / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D012313:RNA