Literature DB >> 22238257

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

Thomas Hentrich1, Julia M Schulze, Eldon Emberly, Michael S Kobor.   

Abstract

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.

Mesh:

Substances:

Year:  2012        PMID: 22238257     DOI: 10.1093/bioinformatics/bts007

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  10 in total

1.  Histone H3 lysine 36 methylation targets the Isw1b remodeling complex to chromatin.

Authors:  Vicki E Maltby; Benjamin J E Martin; Julia M Schulze; Ian Johnson; Thomas Hentrich; Aishwariya Sharma; Michael S Kobor; LeAnn Howe
Journal:  Mol Cell Biol       Date:  2012-07-02       Impact factor: 4.272

2.  Eaf5/7/3 form a functionally independent NuA4 submodule linked to RNA polymerase II-coupled nucleosome recycling.

Authors:  Dorine Rossetto; Myriam Cramet; Alice Y Wang; Anne-Lise Steunou; Nicolas Lacoste; Julia M Schulze; Valérie Côté; Julie Monnet-Saksouk; Sandra Piquet; Amine Nourani; Michael S Kobor; Jacques Côté
Journal:  EMBO J       Date:  2014-05-19       Impact factor: 11.598

3.  High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8.

Authors:  Maria J Aristizabal; Gian Luca Negri; Joris J Benschop; Frank C P Holstege; Nevan J Krogan; Michael S Kobor
Journal:  PLoS Genet       Date:  2013-08-29       Impact factor: 5.917

4.  RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability.

Authors:  Emily Yun-Chia Chang; Carolina A Novoa; Maria J Aristizabal; Yan Coulombe; Romulo Segovia; Richa Chaturvedi; Yaoqing Shen; Christelle Keong; Annie S Tam; Steven J M Jones; Jean-Yves Masson; Michael S Kobor; Peter C Stirling
Journal:  J Cell Biol       Date:  2017-10-17       Impact factor: 10.539

5.  Distinct histone methylation and transcription profiles are established during the development of cellular quiescence in yeast.

Authors:  Conor P Young; Cory Hillyer; Karsten Hokamp; Darren J Fitzpatrick; Nikifor K Konstantinov; Jacqueline S Welty; Scott A Ness; Margaret Werner-Washburne; Alastair B Fleming; Mary Ann Osley
Journal:  BMC Genomics       Date:  2017-01-26       Impact factor: 3.969

6.  C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.

Authors:  Divya Tej Sowpati; Surabhi Srivastava; Jyotsna Dhawan; Rakesh K Mishra
Journal:  BMC Bioinformatics       Date:  2017-09-13       Impact factor: 3.169

7.  HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures.

Authors:  Hani Z Girgis; Alfredo Velasco; Zachary E Reyes
Journal:  BMC Bioinformatics       Date:  2018-09-03       Impact factor: 3.169

8.  MRE11-RAD50-NBS1 promotes Fanconi Anemia R-loop suppression at transcription-replication conflicts.

Authors:  Emily Yun-Chia Chang; Shuhe Tsai; Maria J Aristizabal; James P Wells; Yan Coulombe; Franciele F Busatto; Yujia A Chan; Arun Kumar; Yi Dan Zhu; Alan Ying-Hsu Wang; Louis-Alexandre Fournier; Philip Hieter; Michael S Kobor; Jean-Yves Masson; Peter C Stirling
Journal:  Nat Commun       Date:  2019-09-19       Impact factor: 14.919

9.  Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip.

Authors:  Yujia A Chan; Maria J Aristizabal; Phoebe Y T Lu; Zongli Luo; Akil Hamza; Michael S Kobor; Peter C Stirling; Philip Hieter
Journal:  PLoS Genet       Date:  2014-04-17       Impact factor: 5.917

10.  The RNAPII-CTD Maintains Genome Integrity through Inhibition of Retrotransposon Gene Expression and Transposition.

Authors:  Maria J Aristizabal; Gian Luca Negri; Michael S Kobor
Journal:  PLoS Genet       Date:  2015-10-23       Impact factor: 5.917

  10 in total

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