Literature DB >> 27863955

The BLUEPRINT Data Analysis Portal.

José María Fernández1, Victor de la Torre1, David Richardson2, Romina Royo3, Montserrat Puiggròs4, Valentí Moncunill4, Stamatina Fragkogianni4, Laura Clarke2, Paul Flicek2, Daniel Rico5, David Torrents6, Enrique Carrillo de Santa Pau7, Alfonso Valencia8.   

Abstract

The impact of large and complex epigenomic datasets on biological insights or clinical applications is limited by the lack of accessibility by easy, intuitive, and fast tools. Here, we describe an epigenomics comparative cyber-infrastructure (EPICO), an open-access reference set of libraries to develop comparative epigenomic data portals. Using EPICO, large epigenome projects can make available their rich datasets to the community without requiring specific technical skills. As a first instance of EPICO, we implemented the BLUEPRINT Data Analysis Portal (BDAP). BDAP provides a desktop for the comparative analysis of epigenomes of hematopoietic cell types based on results, such as the position of epigenetic features, from basic analysis pipelines. The BDAP interface facilitates interactive exploration of genomic regions, genes, and pathways in the context of differentiation of hematopoietic lineages. This work represents initial steps toward broadly accessible integrative analysis of epigenomic data across international consortia. EPICO can be accessed at https://github.com/inab, and BDAP can be accessed at http://blueprint-data.bsc.es. Copyright Â
© 2016 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  BLUEPRINT Data Analysis Portal; BLUEPRINT epigenomes; International Human Epigenomes Consortium; bioinformatics; cyber-infrastructure; epigenomic data mining tools; epigenomic data visualization; epigenomics; hematopoiesis; leukemia

Mesh:

Year:  2016        PMID: 27863955      PMCID: PMC5919098          DOI: 10.1016/j.cels.2016.10.021

Source DB:  PubMed          Journal:  Cell Syst        ISSN: 2405-4712            Impact factor:   10.304


  15 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

2.  Modeling sample variables with an Experimental Factor Ontology.

Authors:  James Malone; Ele Holloway; Tomasz Adamusiak; Misha Kapushesky; Jie Zheng; Nikolay Kolesnikov; Anna Zhukova; Alvis Brazma; Helen Parkinson
Journal:  Bioinformatics       Date:  2010-03-03       Impact factor: 6.937

Review 3.  International Union of Basic and Clinical Pharmacology. LXXIII. Nomenclature for the formyl peptide receptor (FPR) family.

Authors:  Richard D Ye; François Boulay; Ji Ming Wang; Claes Dahlgren; Craig Gerard; Marc Parmentier; Charles N Serhan; Philip M Murphy
Journal:  Pharmacol Rev       Date:  2009-06-04       Impact factor: 25.468

4.  BLUEPRINT to decode the epigenetic signature written in blood.

Authors:  David Adams; Lucia Altucci; Stylianos E Antonarakis; Juan Ballesteros; Stephan Beck; Adrian Bird; Christoph Bock; Bernhard Boehm; Elias Campo; Andrea Caricasole; Fredrik Dahl; Emmanouil T Dermitzakis; Tariq Enver; Manel Esteller; Xavier Estivill; Anne Ferguson-Smith; Jude Fitzgibbon; Paul Flicek; Claudia Giehl; Thomas Graf; Frank Grosveld; Roderic Guigo; Ivo Gut; Kristian Helin; Jonas Jarvius; Ralf Küppers; Hans Lehrach; Thomas Lengauer; Åke Lernmark; David Leslie; Markus Loeffler; Elizabeth Macintyre; Antonello Mai; Joost H A Martens; Saverio Minucci; Willem H Ouwehand; Pier Giuseppe Pelicci; Hèléne Pendeville; Bo Porse; Vardhman Rakyan; Wolf Reik; Martin Schrappe; Dirk Schübeler; Martin Seifert; Reiner Siebert; David Simmons; Nicole Soranzo; Salvatore Spicuglia; Michael Stratton; Hendrik G Stunnenberg; Amos Tanay; David Torrents; Alfonso Valencia; Edo Vellenga; Martin Vingron; Jörn Walter; Spike Willcocks
Journal:  Nat Biotechnol       Date:  2012-03-07       Impact factor: 54.908

5.  APPRIS: annotation of principal and alternative splice isoforms.

Authors:  Jose Manuel Rodriguez; Paolo Maietta; Iakes Ezkurdia; Alessandro Pietrelli; Jan-Jaap Wesselink; Gonzalo Lopez; Alfonso Valencia; Michael L Tress
Journal:  Nucleic Acids Res       Date:  2012-11-17       Impact factor: 16.971

6.  An ontology for cell types.

Authors:  Jonathan Bard; Seung Y Rhee; Michael Ashburner
Journal:  Genome Biol       Date:  2005-01-14       Impact factor: 13.583

7.  CLO: The cell line ontology.

Authors:  Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Terrence F Meehan; Alexander D Diehl; Uma D Vempati; Stephan C Schürer; Chao Pang; James Malone; Helen Parkinson; Yue Liu; Terue Takatsuki; Kaoru Saijo; Hiroshi Masuya; Yukio Nakamura; Matthew H Brush; Melissa A Haendel; Jie Zheng; Christian J Stoeckert; Bjoern Peters; Christopher J Mungall; Thomas E Carey; David J States; Brian D Athey; Yongqun He
Journal:  J Biomed Semantics       Date:  2014-08-13

8.  Ensembl 2014.

Authors:  Paul Flicek; M Ridwan Amode; Daniel Barrell; Kathryn Beal; Konstantinos Billis; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Stephen Fitzgerald; Laurent Gil; Carlos García Girón; Leo Gordon; Thibaut Hourlier; Sarah Hunt; Nathan Johnson; Thomas Juettemann; Andreas K Kähäri; Stephen Keenan; Eugene Kulesha; Fergal J Martin; Thomas Maurel; William M McLaren; Daniel N Murphy; Rishi Nag; Bert Overduin; Miguel Pignatelli; Bethan Pritchard; Emily Pritchard; Harpreet S Riat; Magali Ruffier; Daniel Sheppard; Kieron Taylor; Anja Thormann; Stephen J Trevanion; Alessandro Vullo; Steven P Wilder; Mark Wilson; Amonida Zadissa; Bronwen L Aken; Ewan Birney; Fiona Cunningham; Jennifer Harrow; Javier Herrero; Tim J P Hubbard; Rhoda Kinsella; Matthieu Muffato; Anne Parker; Giulietta Spudich; Andy Yates; Daniel R Zerbino; Stephen M J Searle
Journal:  Nucleic Acids Res       Date:  2013-12-06       Impact factor: 16.971

9.  Ontology based molecular signatures for immune cell types via gene expression analysis.

Authors:  Terrence F Meehan; Nicole A Vasilevsky; Christopher J Mungall; David S Dougall; Melissa A Haendel; Judith A Blake; Alexander D Diehl
Journal:  BMC Bioinformatics       Date:  2013-08-30       Impact factor: 3.169

10.  The Reactome pathway knowledgebase.

Authors:  David Croft; Antonio Fabregat Mundo; Robin Haw; Marija Milacic; Joel Weiser; Guanming Wu; Michael Caudy; Phani Garapati; Marc Gillespie; Maulik R Kamdar; Bijay Jassal; Steven Jupe; Lisa Matthews; Bruce May; Stanislav Palatnik; Karen Rothfels; Veronica Shamovsky; Heeyeon Song; Mark Williams; Ewan Birney; Henning Hermjakob; Lincoln Stein; Peter D'Eustachio
Journal:  Nucleic Acids Res       Date:  2013-11-15       Impact factor: 16.971

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  50 in total

1.  Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome.

Authors:  Martin Wegner; Valentina Diehl; Verena Bittl; Rahel de Bruyn; Svenja Wiechmann; Yves Matthess; Marie Hebel; Michael Gb Hayes; Simone Schaubeck; Christopher Benner; Sven Heinz; Anja Bremm; Ivan Dikic; Andreas Ernst; Manuel Kaulich
Journal:  Elife       Date:  2019-03-06       Impact factor: 8.140

Review 2.  Translational Perspective on Epigenetics in Cardiovascular Disease.

Authors:  Pim van der Harst; Leon J de Windt; John C Chambers
Journal:  J Am Coll Cardiol       Date:  2017-08-01       Impact factor: 24.094

3.  Identification of the Regulatory Elements and Target Genes of Megakaryopoietic Transcription Factor MEF2C.

Authors:  Xianguo Kong; Lin Ma; Edward Chen; Chad A Shaw; Leonard C Edelstein
Journal:  Thromb Haemost       Date:  2019-02-07       Impact factor: 5.249

4.  GENCODE Pseudogenes.

Authors:  Cristina Sisu
Journal:  Methods Mol Biol       Date:  2021

5.  Convolutional neural network model to predict causal risk factors that share complex regulatory features.

Authors:  Taeyeop Lee; Min Kyung Sung; Seulkee Lee; Woojin Yang; Jaeho Oh; Jeong Yeon Kim; Seongwon Hwang; Hyo-Jeong Ban; Jung Kyoon Choi
Journal:  Nucleic Acids Res       Date:  2019-12-16       Impact factor: 16.971

Review 6.  Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives.

Authors:  Wolfgang Poller; Stefanie Dimmeler; Stephane Heymans; Tanja Zeller; Jan Haas; Mahir Karakas; David-Manuel Leistner; Philipp Jakob; Shinichi Nakagawa; Stefan Blankenberg; Stefan Engelhardt; Thomas Thum; Christian Weber; Benjamin Meder; Roger Hajjar; Ulf Landmesser
Journal:  Eur Heart J       Date:  2018-08-01       Impact factor: 29.983

7.  A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection.

Authors:  Alexandre Pellan Cheng; Philip Burnham; John Richard Lee; Matthew Pellan Cheng; Manikkam Suthanthiran; Darshana Dadhania; Iwijn De Vlaminck
Journal:  Proc Natl Acad Sci U S A       Date:  2019-08-26       Impact factor: 11.205

8.  Single-cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL.

Authors:  Praveen Anand; Amy Guillaumet-Adkins; Valeriya Dimitrova; Huiyoung Yun; Yotam Drier; Noori Sotudeh; Anna Rogers; Madhu M Ouseph; Monica Nair; Sayalee Potdar; Randi Isenhart; Jake A Kloeber; Tushara Vijaykumar; Leili Niu; Tiffaney Vincent; Guangwu Guo; Julia Frede; Marian H Harris; Andrew E Place; Lewis B Silverman; David T Teachey; Andrew A Lane; Daniel J DeAngelo; Jon C Aster; Bradley E Bernstein; Jens G Lohr; Birgit Knoechel
Journal:  Blood       Date:  2021-05-06       Impact factor: 22.113

9.  DNA Methylome Alterations Are Associated with Airway Macrophage Differentiation and Phenotype during Lung Fibrosis.

Authors:  Peter McErlean; Christopher G Bell; Richard J Hewitt; Zabreen Busharat; Patricia P Ogger; Poonam Ghai; Gesa J Albers; Emily Calamita; Shaun Kingston; Philip L Molyneaux; Stephan Beck; Clare M Lloyd; Toby M Maher; Adam J Byrne
Journal:  Am J Respir Crit Care Med       Date:  2021-10-15       Impact factor: 21.405

10.  The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability.

Authors:  Jennifer Derrien; Catherine Guérin-Charbonnel; Victor Gaborit; Loïc Campion; Magali Devic; Elise Douillard; Nathalie Roi; Hervé Avet-Loiseau; Olivier Decaux; Thierry Facon; Jan-Philipp Mallm; Roland Eils; Nikhil C Munshi; Philippe Moreau; Carl Herrmann; Florence Magrangeas; Stéphane Minvielle
Journal:  Genome Med       Date:  2021-08-09       Impact factor: 11.117

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