Literature DB >> 33816851

Enhort: a platform for deep analysis of genomic positions.

Michael Menzel1, Peter Koch1, Stefan Glasenhardt1, Andreas Gogol-Döring1.   

Abstract

The rise of high-throughput methods in genomic research greatly expanded our knowledge about the functionality of the genome. At the same time, the amount of available genomic position data increased massively, e.g., through genome-wide profiling of protein binding, virus integration or DNA methylation. However, there is no specialized software to investigate integration site profiles of virus integration or transcription factor binding sites by correlating the sites with the diversity of available genomic annotations. Here we present Enhort, a user-friendly software tool for relating large sets of genomic positions to a variety of annotations. It functions as a statistics based genome browser, not focused on a single locus but analyzing many genomic positions simultaneously. Enhort provides comprehensive yet easy-to-use methods for statistical analysis, visualization, and the adjustment of background models according to experimental conditions and scientific questions. Enhort is publicly available online at enhort.mni.thm.de and published under GNU General Public License. ©2019 Menzel et al.

Entities:  

Keywords:  Data analysis; Genome annotation; Integration profiling; Next-generation sequencing; Virology

Year:  2019        PMID: 33816851      PMCID: PMC7924414          DOI: 10.7717/peerj-cs.198

Source DB:  PubMed          Journal:  PeerJ Comput Sci        ISSN: 2376-5992


  26 in total

1.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

Review 2.  HIV DNA integration.

Authors:  Robert Craigie; Frederic D Bushman
Journal:  Cold Spring Harb Perspect Med       Date:  2012-07       Impact factor: 6.915

3.  Highly divergent integration profile of adeno-associated virus serotype 5 revealed by high-throughput sequencing.

Authors:  Tyler Janovitz; Thiago Oliveira; Michel Sadelain; Erik Falck-Pedersen
Journal:  J Virol       Date:  2013-12-11       Impact factor: 5.103

4.  PiggyBac transposon-mediated gene transfer in human cells.

Authors:  Matthew H Wilson; Craig J Coates; Alfred L George
Journal:  Mol Ther       Date:  2007-01       Impact factor: 11.454

Review 5.  Virus integration and genome influence in approaches to stem cell based therapy for andro-urology.

Authors:  Longkun Li; Deying Zhang; Peng Li; Margot Damaser; Yuanyuan Zhang
Journal:  Adv Drug Deliv Rev       Date:  2014-10-18       Impact factor: 15.470

Review 6.  Adeno-associated virus vector integration.

Authors:  David R Deyle; David W Russell
Journal:  Curr Opin Mol Ther       Date:  2009-08

7.  Integrative genomics viewer.

Authors:  James T Robinson; Helga Thorvaldsdóttir; Wendy Winckler; Mitchell Guttman; Eric S Lander; Gad Getz; Jill P Mesirov
Journal:  Nat Biotechnol       Date:  2011-01       Impact factor: 54.908

8.  The Genomic HyperBrowser: an analysis web server for genome-scale data.

Authors:  Geir K Sandve; Sveinung Gundersen; Morten Johansen; Ingrid K Glad; Krishanthi Gunathasan; Lars Holden; Marit Holden; Knut Liestøl; Ståle Nygård; Vegard Nygaard; Jonas Paulsen; Halfdan Rydbeck; Kai Trengereid; Trevor Clancy; Finn Drabløs; Egil Ferkingstad; Matús Kalas; Tonje Lien; Morten B Rye; Arnoldo Frigessi; Eivind Hovig
Journal:  Nucleic Acids Res       Date:  2013-04-30       Impact factor: 16.971

9.  Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.

Authors:  Ryan K Dale; Brent S Pedersen; Aaron R Quinlan
Journal:  Bioinformatics       Date:  2011-09-23       Impact factor: 6.937

10.  Genome-wide Profiling Reveals Remarkable Parallels Between Insertion Site Selection Properties of the MLV Retrovirus and the piggyBac Transposon in Primary Human CD4(+) T Cells.

Authors:  Andreas Gogol-Döring; Ismahen Ammar; Saumyashree Gupta; Mario Bunse; Csaba Miskey; Wei Chen; Wolfgang Uckert; Thomas F Schulz; Zsuzsanna Izsvák; Zoltán Ivics
Journal:  Mol Ther       Date:  2016-01-12       Impact factor: 11.454

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