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EpiGRAPH user-friendly software for statistical analysis and prediction of (epi)genomic data.doc

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EpiGRAPH user-friendly software for statistical analysis and prediction of (epi)genomic data

Open Access 2009BocketVSoal.lumeftw10,areIssue 2, Article R14 EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data Christoph Bock, Konstantin Halachev, Joachim Büch and Thomas Lengauer Address: Max-Planck-Institut für Informatik, Campus E1.4, 66123 Saarbrücken, Germany. Correspondence: Christoph Bock. Email: cbock@mpi-inf.mpg.de Published: 10 February 2009 Received: 18 June 2008 Revised: 3 December 2008 Accepted: 10 February 2009 Genome Biology 2009, 10:R14 (doi:10.1186/gb-2009-10-2-r14) The electronic version of this article is the complete one and can be found online at /2009/10/2/R14 ? 2009 Bock et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. EpiGRAPHdatEpiGRAPHasets of genomis iacgenome-scaleregions./p data-mining software tool that enables users to identify epigenetic and gene regulatory features in large Abstract The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutionary conservation) for enrichment or depletion among these regions. Furthermore, EpiGRAPH learns to predictively identify similar genomic regions. This paper demonstrates EpiGRAPHs practical utility in a case study on monoallelic gene expression and describes its novel approach to reproducible bioinformatic analysis. Rationale located outside of (protein-coding) genes. In the absence of a suitable tool for statistical analysis and prediction of genomic region data, researchers have performed the necessary steps by hand, down