Reference : Analysis of the dynamic co-expression network of heart regeneration in the zebrafish

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Multidisciplinary, general & others
	Focus Areas :	Systems Biomedicine
	To cite this reference:	http://hdl.handle.net/10993/27815

Title :	Analysis of the dynamic co-expression network of heart regeneration in the zebrafish
Language :	English
Author, co-author :	Rodius, Sophie [Luxembourg Institute of Health (LIH) > Oncology Department > NorLux Neuro-Oncology Laboratory]
	Androsova, Ganna [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; Luxembourg Institute of Health (LIH) > Oncology Department > NorLux Neuro-Oncology Laboratory]
	Götz, Lou [SIB Swiss Institute of Bioinformatics > Vital-IT Systems Biology Division]
	Liechti, Robin [SIB Swiss Institute of Bioinformatics > Vital-IT Systems Biology Division]
	Crespo, Isaac [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; SIB Swiss Institute of Bioinformatics > Vital-IT Systems Biology Division]
	Merz, Susanne [Luxembourg Institute of Health (LIH) > Oncology Department > NorLux Neuro-Oncology Laboratory]
	Nazarov, Petr [Luxembourg Institute of Health (LIH) > Oncology Department > Genomics Research Unit]
	de Klein, Niek [Luxembourg Institute of Health (LIH) > Oncology Department > NorLux Neuro-Oncology Laboratory > ; Vrije Universiteit Amsterdam - VU > > > ; University of Groningen > Department of Genetics]
	Jeanty, Céline [Luxembourg Institute of Health (LIH) > Oncology Department > NorLux Neuro-Oncology Laboratory]
	González-Rosa, Juan [Cardiovascular Research Center]
	Muller, Arnaud [Luxembourg Institute of Health (LIH) > Oncology Department > Genomics Research Unit]
	Bernardin, Francois [Luxembourg Institute of Health (LIH) > Oncology Department > Genomics Research Unit]
	Niclou, Simone [Luxembourg Institute of Health (LIH) > Oncology Department > NorLux Neuro-Oncology Laboratory]
	Vallar, Laurent [Luxembourg Institute of Health (LIH) > Oncology Department > Genomics Research Unit]
	Mercader, Nadia [Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) > Epicardium Development and Regeneration group > > ; University of Bern > Faculty of Medicine > Institute of Anatomy > Department of Development and Regeneration]
	Ibberson, Mark [SIB Swiss Institute of Bioinformatics > Vital-IT Systems Biology Division]
	Xenarios, Ioannis [SIB Swiss Institute of Bioinformatics > Vital-IT Systems Biology Division > > ; University of Lausanne > Center for Integrative Genomics > > ; University of Geneva > Department of Biochemistry]
	Azuaje, Francisco [Luxembourg Institute of Health (LIH) > Oncology Department > NorLux Neuro-Oncology Laboratory]
Publication date :	31-May-2016
Journal title :	Scientific Reports
Publisher :	Nature Publishing Group
Volume :	6
Peer reviewed :	Yes (verified by ORBilu)
Audience :	International
e-ISSN :	2045-2322
City :	London
Country :	United Kingdom
Keywords :	[en] Network topology ; Regulatory networks ; Transcriptomics
Abstract :	[en] The zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration.
Funders :	Luxembourg’s National Research Fund (FNR), Swiss National Research Foundation (SNF)
Name of the research project :	INFUSED
Target :	Researchers ; Professionals ; Students
Permalink :	http://hdl.handle.net/10993/27815
DOI :	10.1038/srep26822
Other URL :	http://www.nature.com/articles/srep26822#abstract

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