Warning: The NCBI web site requires JavaScript to function. more...

My NCBI Sign In

Result Filters

Genome Biol. 2009 Feb 10;10(2):R14.

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

Bock C, Halachev K, Büch J, Lengauer T.

Source

Max-Planck-Institut für Informatik, Campus E1.4, 66123 Saarbrücken, Germany. cbock@mpi-inf.mpg.de

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

PMID:: 19208250; [PubMed - indexed for MEDLINE]
PMCID:: PMC2688269

Free PMC Article

Images from this publication.See all images (5) Free text

Publication Types, MeSH Terms

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Icon for BioMed Central

Icon for PubMed Central

Save items

loading

Related citations in PubMed

Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy. [Methods Mol Biol. 2010]
Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy.
Bock C, Von Kuster G, Halachev K, Taylor J, Nekrutenko A, Lengauer T. Methods Mol Biol. 2010; 628:275-96.
The missing graphical user interface for genomics. [Genome Biol. 2010]
The missing graphical user interface for genomics.
Schatz MC. Genome Biol. 2010; 11(8):128. Epub 2010 Aug 25.
JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow. [BMC Bioinformatics. 2006]
JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.
Latorre M, Silva H, Saba J, Guziolowski C, Vizoso P, Martinez V, Maldonado J, Morales A, Caroca R, Cambiazo V, et al. BMC Bioinformatics. 2006 Nov 23; 7:513. Epub 2006 Nov 23.
Review The UCSC genome browser: what every molecular biologist should know. [Curr Protoc Mol Biol. 2009]
Review The UCSC genome browser: what every molecular biologist should know.
Mangan ME, Williams JM, Kuhn RM, Lathe WC 3rd. Curr Protoc Mol Biol. 2009 Oct; Chapter 19:Unit19.9.
Review Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA. [Nat Immunol. 2004]
Review Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA.
Nardone J, Lee DU, Ansel KM, Rao A. Nat Immunol. 2004 Aug; 5(8):768-74.

See reviews... See all...

Cited by 9 PubMed Central articles

Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. [Nat Genet. 2011]
Dynamic CpG island methylation landscape in oocytes and preimplantation embryos.
Smallwood SA, Tomizawa S, Krueger F, Ruf N, Carli N, Segonds-Pichon A, Sato S, Hata K, Andrews SR, Kelsey G. Nat Genet. 2011 Jun 26; 43(8):811-4. Epub 2011 Jun 26.
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. [Cell. 2011]
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines.
Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, et al. Cell. 2011 Feb 4; 144(3):439-52.
The Genomic HyperBrowser: inferential genomics at the sequence level. [Genome Biol. 2010]
The Genomic HyperBrowser: inferential genomics at the sequence level.
Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Ferkingstad E, Johansen M, et al. Genome Biol. 2010; 11(12):R121. Epub 2010 Dec 23.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi...
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.
Genome Biol. 2009 Feb 10 ;10(2):R14.

PubMed
Meta-analysis of duloxetine vs. pregabalin and gabapentin in the treatment of di...
Meta-analysis of duloxetine vs. pregabalin and gabapentin in the treatment of diabetic peripheral neuropathic pain.
BMC Neurol. 2009 Feb 10 ;9:6.

PubMed
Knowledge about human papillomavirus and the HPV vaccine--a survey of the genera...
Knowledge about human papillomavirus and the HPV vaccine--a survey of the general population.
Infect Agent Cancer. 2009 Feb 10 ;4 Suppl 1:S10.

PubMed
Co-evolution positions and rules for antigenic variants of human influenza A/H3N...
Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses.
BMC Bioinformatics. 2009 Jan 30 ;10 Suppl 1:S41.

PubMed
Computational identification of condition-specific miRNA targets based on gene e...
Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information.
BMC Bioinformatics. 2009 Jan 30 ;10 Suppl 1:S34.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

You are here: NCBI > Literature > PubMed

Write to the Help Desk