Literature DB >> 19208250

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

Christoph Bock1, Konstantin Halachev, Joachim Büch, Thomas Lengauer.   

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.

Entities:  

Mesh：

Year:  2009        PMID： 19208250      PMCID： PMC2688269          DOI： 10.1186/gb-2009-10-2-r14

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  47 in total

1.  Computational prediction of methylation status in human genomic sequences.

Authors:  Rajdeep Das; Nevenka Dimitrova; Zhenyu Xuan; Robert A Rollins; Fatemah Haghighi; John R Edwards; Jingyue Ju; Timothy H Bestor; Michael Q Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2006-07-03       Impact factor: 11.205

2.  Computational and experimental identification of novel human imprinted genes.

Authors:  Philippe P Luedi; Fred S Dietrich; Jennifer R Weidman; Jason M Bosko; Randy L Jirtle; Alexander J Hartemink
Journal:  Genome Res       Date:  2007-11-30       Impact factor: 9.043

Review 3.  Computational epigenetics.

Authors:  Christoph Bock; Thomas Lengauer
Journal:  Bioinformatics       Date:  2007-11-17       Impact factor: 6.937

4.  A novel approach for identifying candidate imprinted genes through sequence analysis of imprinted and control genes.

Authors:  Xiayi Ke; N Simon Thomas; David O Robinson; Andrew Collins
Journal:  Hum Genet       Date:  2002-09-13       Impact factor: 4.132

5.  An isochore map of human chromosomes.

Authors:  Maria Costantini; Oliver Clay; Fabio Auletta; Giorgio Bernardi
Journal:  Genome Res       Date:  2006-04       Impact factor: 9.043

6.  GSEA-P: a desktop application for Gene Set Enrichment Analysis.

Authors:  Aravind Subramanian; Heidi Kuehn; Joshua Gould; Pablo Tamayo; Jill P Mesirov
Journal:  Bioinformatics       Date:  2007-07-20       Impact factor: 6.937

7.  Selection of target sites for mobile DNA integration in the human genome.

Authors:  Charles Berry; Sridhar Hannenhalli; Jeremy Leipzig; Frederic D Bushman
Journal:  PLoS Comput Biol       Date:  2006-11-24       Impact factor: 4.475

8.  A survey of genomic properties for the detection of regulatory polymorphisms.

Authors:  Stephen B Montgomery; Obi L Griffith; Johanna M Schuetz; Angela Brooks-Wilson; Steven J M Jones
Journal:  PLoS Comput Biol       Date:  2007-04-25       Impact factor: 4.475

9.  CpG island mapping by epigenome prediction.

Authors:  Christoph Bock; Jörn Walter; Martina Paulsen; Thomas Lengauer
Journal:  PLoS Comput Biol       Date:  2007-05-02       Impact factor: 4.475

Review 10.  Machine learning and its applications to biology.

Authors:  Adi L Tarca; Vincent J Carey; Xue-wen Chen; Roberto Romero; Sorin Drăghici
Journal:  PLoS Comput Biol       Date:  2007-06       Impact factor: 4.475
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  26 in total

1.  Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage.

Authors:  Lukas Chavez; Justyna Jozefczuk; Christina Grimm; Jörn Dietrich; Bernd Timmermann; Hans Lehrach; Ralf Herwig; James Adjaye
Journal:  Genome Res       Date:  2010-08-27       Impact factor: 9.043

2.  Processing and analyzing ChIP-seq data: from short reads to regulatory interactions.

Authors:  Marion Leleu; Grégory Lefebvre; Jacques Rougemont
Journal:  Brief Funct Genomics       Date:  2010-09-22       Impact factor: 4.241

3.  Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis.

Authors:  Shicai Fan; Chengzhe Li; Rizi Ai; Mengchi Wang; Gary S Firestein; Wei Wang
Journal:  Bioinformatics       Date:  2016-02-15       Impact factor: 6.937

Review 4.  Recommendations for the design and analysis of epigenome-wide association studies.

Authors:  Karin B Michels; Alexandra M Binder; Sarah Dedeurwaerder; Charles B Epstein; John M Greally; Ivo Gut; E Andres Houseman; Benedetta Izzi; Karl T Kelsey; Alexander Meissner; Aleksandar Milosavljevic; Kimberly D Siegmund; Christoph Bock; Rafael A Irizarry
Journal:  Nat Methods       Date:  2013-10       Impact factor: 28.547

5.  Mutant p53 is a transcriptional co-factor that binds to G-rich regulatory regions of active genes and generates transcriptional plasticity.

Authors:  Timo Quante; Benjamin Otto; Marie Brázdová; Iva Kejnovská; Wolfgang Deppert; Genrich V Tolstonog
Journal:  Cell Cycle       Date:  2012-08-21       Impact factor: 4.534

Review 6.  Analysing and interpreting DNA methylation data.

Authors:  Christoph Bock
Journal:  Nat Rev Genet       Date:  2012-10       Impact factor: 53.242

7.  Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines.

Authors:  Christoph Bock; Evangelos Kiskinis; Griet Verstappen; Hongcang Gu; Gabriella Boulting; Zachary D Smith; Michael Ziller; Gist F Croft; Mackenzie W Amoroso; Derek H Oakley; Andreas Gnirke; Kevin Eggan; Alexander Meissner
Journal:  Cell       Date:  2011-02-04       Impact factor: 41.582

8.  GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.

Authors:  Boris Simovski; Daniel Vodák; Sveinung Gundersen; Diana Domanska; Abdulrahman Azab; Lars Holden; Marit Holden; Ivar Grytten; Knut Rand; Finn Drabløs; Morten Johansen; Antonio Mora; Christin Lund-Andersen; Bastian Fromm; Ragnhild Eskeland; Odd Stokke Gabrielsen; Egil Ferkingstad; Sigve Nakken; Mads Bengtsen; Alexander Johan Nederbragt; Hildur Sif Thorarensen; Johannes Andreas Akse; Ingrid Glad; Eivind Hovig; Geir Kjetil Sandve
Journal:  Gigascience       Date:  2017-07-01       Impact factor: 6.524

9.  MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays.

Authors:  Peter Schüffler; Thomas Mikeska; Andreas Waha; Thomas Lengauer; Christoph Bock
Journal:  Genome Biol       Date:  2009-10-05       Impact factor: 13.583

10.  Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.

Authors:  Hongcang Gu; Christoph Bock; Tarjei S Mikkelsen; Natalie Jäger; Zachary D Smith; Eleni Tomazou; Andreas Gnirke; Eric S Lander; Alexander Meissner
Journal:  Nat Methods       Date:  2010-01-10       Impact factor: 28.547
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