CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures

UNLABELLED CHROMATRA (CHROmatin Mapping Across TRAnscripts) is a visualization tool available as plug-in for the Galaxy platform. It allows detailed yet concise presentations of data derived from ChIP-chip or ChIP-seq experiments by visualizing enrichment scores across genes or other genomic features while accounting for their length and additional characteristics such as gene expression. It integrates into typical analysis workflows and enables rapid graphical assessment and comparison of genome-wide data at a glance. AVAILABILITY https://github.com/cmmt/chromatra.

[1]  Megan F. Cole,et al.  Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.

[2]  Julia M. Schulze,et al.  Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation , 2009, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Daniel J. Blankenberg,et al.  A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. , 2007, Genome research.

[4]  R. Stoughton Applications of DNA microarrays in biology. , 2005, Annual review of biochemistry.

[5]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[6]  M. Metzker Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[7]  P. Collas The Current State of Chromatin Immunoprecipitation , 2010, Molecular biotechnology.

[8]  W. Lam,et al.  Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells , 2005, Nature Genetics.

[9]  Michael R. Green,et al.  Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.

[10]  T. Gingeras,et al.  Genome-wide transcription and the implications for genomic organization , 2007, Nature Reviews Genetics.

[11]  Johannes Söding,et al.  Uniform transitions of the general RNA polymerase II transcription complex , 2010, Nature Structural &Molecular Biology.

[12]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[13]  Matthew A. Hibbs,et al.  Visualization of omics data for systems biology , 2010, Nature Methods.

[14]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[15]  David Serre,et al.  MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome , 2009, Nucleic acids research.

[16]  Julia M. Schulze,et al.  Splitting the task: Ubp8 and Ubp10 deubiquitinate different cellular pools of H2BK123. , 2011, Genes & development.

[17]  Esteban Ballestar,et al.  Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. , 2008, BioTechniques.

[18]  David Haussler,et al.  The UCSC Genome Browser database: update 2010 , 2009, Nucleic Acids Res..

[19]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..