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

Max-Planck-Institut für Informatik, Campus E1.4, 66123 Saarbrücken, Germany.
Genome biology (Impact Factor: 10.81). 03/2009; 10(2):R14. DOI: 10.1186/gb-2009-10-2-r14
Source: PubMed


The EpiGRAPH web service 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 EpiGRAPH's practical utility in a case study on monoallelic gene expression and describes its novel approach to reproducible bioinformatic analysis.

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Available from: Konstantin Halachev,
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    • "(D) Functional and structural characteristics of the 1000 most variable genes in terms of DNA methylation (left) and gene expression (right). Functional annotation clustering was performed with the DAVID software (Huang et al., 2007), and the promoter characteristics were analyzed by the EpiGRAPH web service (Bock et al., 2009). This panel provides a summary of the results; the full results tables are available online "
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    Cell 02/2011; 144(3):439-52. DOI:10.1016/j.cell.2010.12.032 · 32.24 Impact Factor
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    • "For example, numerous tools, integrated or not in larger analysis pipelines, have been proposed that allow: annotation of genomic features present in the neighbourhood of the relevant enrichment signals (5–7), detection and de novo definition of consensus DNA motifs (6), cross and compare information from distinct datasets (8) and comprehensive visualization of the obtained GW results (9–11). More recently, sophisticated statistical approaches were proposed to predict association between sets of genomic locations and numerous genomic features (12,13). Nevertheless, due to the multiplicity of biological questions that may be asked by the ChIP-seq method, many analysis issues remain un-addressed. "
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    Nucleic Acids Research 12/2010; 39(6):e35. DOI:10.1093/nar/gkq1287 · 9.11 Impact Factor
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    • "EpiGRAPH ( is an online software to analyze genomic and epigenomic features enriched in a group of given DNA fragments (35–37). EpiGRAPH was used to analyze DNA sequences harboring the differentially methylated CpG sites in CdLS in terms of the specific DNA sequence patterns, the overlap with specific genomic regions (e.g. "
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