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Literature DB >> 23827707

Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers.

Abstract

Over the past years we have witnessed an explosion in the generation of freely available genome-wide data sets, including maps of various histone modifications, transcription factor binding, DNase hypersensitivity, and DNA methylation, which provide valuable resources for data validation, exploration, and hypothesis generation. The goal of this review is to provide the reader with information on where to find many of the data sets and how to utilize the various (epi)genome browsers for display and initial analysis. We provide selected examples to highlight key features and demonstrate the application of these browsers to stem cell biology.

Entities: CellLine Chemical Disease Gene Species

Mesh：

Year: 2013 PMID： 23827707 PMCID： PMC3750740 DOI： 10.1016/j.stem.2013.06.006

Source DB: PubMed Journal: Cell Stem Cell ISSN： 1875-9777 Impact factor: 24.633

40 in total

1. GREAT improves functional interpretation of cis-regulatory regions.

Authors: Cory Y McLean; Dave Bristor; Michael Hiller; Shoa L Clarke; Bruce T Schaar; Craig B Lowe; Aaron M Wenger; Gill Bejerano
Journal: Nat Biotechnol Date: 2010-05-02 Impact factor: 54.908

2. Targeting of de novo DNA methylation throughout the Oct-4 gene regulatory region in differentiating embryonic stem cells.

Authors: Rodoniki Athanasiadou; Dina de Sousa; Kevin Myant; Cara Merusi; Irina Stancheva; Adrian Bird
Journal: PLoS One Date: 2010-04-01 Impact factor: 3.240

3. Touring Ensembl: a practical guide to genome browsing.

Authors: Giulietta M Spudich; Xosé M Fernández-Suárez
Journal: BMC Genomics Date: 2010-05-11 Impact factor: 3.969

4. Human DNA methylomes at base resolution show widespread epigenomic differences.

Authors: Ryan Lister; Mattia Pelizzola; Robert H Dowen; R David Hawkins; Gary Hon; Julian Tonti-Filippini; Joseph R Nery; Leonard Lee; Zhen Ye; Que-Minh Ngo; Lee Edsall; Jessica Antosiewicz-Bourget; Ron Stewart; Victor Ruotti; A Harvey Millar; James A Thomson; Bing Ren; Joseph R Ecker
Journal: Nature Date: 2009-10-14 Impact factor: 49.962

5. Galaxy: a web-based genome analysis tool for experimentalists.

Authors: Daniel Blankenberg; Gregory Von Kuster; Nathaniel Coraor; Guruprasad Ananda; Ross Lazarus; Mary Mangan; Anton Nekrutenko; James Taylor
Journal: Curr Protoc Mol Biol Date: 2010-01

6. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

Authors: Xi Chen; Han Xu; Ping Yuan; Fang Fang; Mikael Huss; Vinsensius B Vega; Eleanor Wong; Yuriy L Orlov; Weiwei Zhang; Jianming Jiang; Yuin-Han Loh; Hock Chuan Yeo; Zhen Xuan Yeo; Vipin Narang; Kunde Ramamoorthy Govindarajan; Bernard Leong; Atif Shahab; Yijun Ruan; Guillaume Bourque; Wing-Kin Sung; Neil D Clarke; Chia-Lin Wei; Huck-Hui Ng
Journal: Cell Date: 2008-06-13 Impact factor: 41.582

7. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Authors: Tarjei S Mikkelsen; Manching Ku; David B Jaffe; Biju Issac; Erez Lieberman; Georgia Giannoukos; Pablo Alvarez; William Brockman; Tae-Kyung Kim; Richard P Koche; William Lee; Eric Mendenhall; Aisling O'Donovan; Aviva Presser; Carsten Russ; Xiaohui Xie; Alexander Meissner; Marius Wernig; Rudolf Jaenisch; Chad Nusbaum; Eric S Lander; Bradley E Bernstein
Journal: Nature Date: 2007-07-01 Impact factor: 49.962

8. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors: Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal: Genome Biol Date: 2010-08-25 Impact factor: 13.583

9. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes.

Authors: Silvina Epsztejn-Litman; Nirit Feldman; Monther Abu-Remaileh; Yoel Shufaro; Ariela Gerson; Jun Ueda; Rachel Deplus; François Fuks; Yoichi Shinkai; Howard Cedar; Yehudit Bergman
Journal: Nat Struct Mol Biol Date: 2008-10-26 Impact factor: 15.369

10. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Authors: Da Wei Huang; Brad T Sherman; Richard A Lempicki
Journal: Nucleic Acids Res Date: 2008-11-25 Impact factor: 16.971

9 in total

1. Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction.

Authors: Andrew D Rouillard; Zichen Wang; Avi Ma'ayan
Journal: Comput Biol Chem Date: 2015-10 Impact factor: 2.877

Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers.

1. GREAT improves functional interpretation of cis-regulatory regions.

2. Targeting of de novo DNA methylation throughout the Oct-4 gene regulatory region in differentiating embryonic stem cells.

3. Touring Ensembl: a practical guide to genome browsing.

4. Human DNA methylomes at base resolution show widespread epigenomic differences.

5. Galaxy: a web-based genome analysis tool for experimentalists.

6. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

7. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

8. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

9. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes.

10. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

1. Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction.

Review 2. The future of neuroepigenetics in the human brain.

3. Toxicoepigenetics for Risk Assessment: Bridging the Gap Between Basic and Regulatory Science.

4. Functional interpretation of non-coding sequence variation: concepts and challenges.

5. Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells.

6. Epigenetic Classification of Human Mesenchymal Stromal Cells.

7. Dynamic Changes in Occupancy of Histone Variant H2A.Z during Induced Somatic Cell Reprogramming.

8. chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome.

9. Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells.