DANIO-CODE
DANIO-CODE is an international collaborative effort that aims to annotate the functional elements of the zebrafish genome.
Zebrafish are increasingly used to successfully model human disease, to screen drugs and to study environmental toxicity in addition to being a model for embryonic development. Zebrafish genome is the third most complete but further annotation is essential to better realize the power of this model organism in diverse areas of biomedical research and to further strengthen its role in biomedical research.
DANIO-CODE partners work together to provide a central resource of publicly available data and genome annotation of the zebrafish genome. DANIO-CODE combines a large variety of genome wide datasets including protein-coding and non-coding transcribed genome elements, non-coding functional elements such as cis-regulatory modules and associated epigenetic features.
DANIO-CODE was established at a workshop held in Imperial College London in December 2014 (see meeting report published in Zebrafish) where members of the zebrafish genomics research community and previous contributors to ENCODE and FANTOM genome annotation projects identified key aims.
The DANIO-CODE key aims
The DANIO-CODE key aims
- Establishment of a Data Coordination Centre for standardised data input into a shared Data Resource. This will provide centralised and convenient access and visualisation of currently inaccessible zebrafish genomics datasets such as ChIP-seq, CAGE-seq, RNA-seq, ATAC-seq, Ribo-seq, meDIP-seq. As a first step, published data is being reanalyzed for GRCz10 by standard pipelines with the aim that data will become mineable through a Track hub hosted by ZFIN and managed by DANIO-CODE partners.
- Identification and generation of common policies on data standardization, integration and data sharing.
- Seeking and obtaining funding through joint ventures for genomics resource generation and management identified as community priorities
- Among the future aims is to establish a consortium agreement and a platform for sharing unpublished data and to work together in community inspired annotation efforts.
The DANIO-CODE Network Partners
The DANIO-CODE Network Partners
- Brad Cairns - Huntsman Cancer Institute, University of Utah, US
- Alena Shkumatava - Institute Curie, France
- Andrea Pauli - The Research Institute of Molecular Pathology, Austria
- Antonio Giraldez - Yale University, US
- Ben Brown - Lawrence Berkeley National Laboratory, Berkeley, US
- Bernard Peers - University of Liege, Belgium
- Boris Lenhard - Imperial College, London, UK
- Carsten Daub - Karolinka Institute, Sweden
- Cecilia Winata - Institute of Molecular & Cell Biology in Warsaw, Poland
- Charles Vejnar - Yale University
- Daria Onitchchouk - University of Freiburg, Germany
- Eivind Valen - Harvard University, US
- Elisabeth Busch - Sanger Institute, Cambridge, UK
- Ferenc Mueller - University of Birmingham, UK
- Fiona Wardle - Kings College London, UK
- Jennifer Harrow - Sanger Institute, Cambridge, UK
- John Colbourne - University of Birmingham, UK
- John Collins - Sanger Institute, Cambridge, UK
- Jose Louis Skarmeta - Grupo Epos, Spain
- Juanma Vaquerizas - Max Planc Institute, Germany
- Julia Horsfield - University of Otago, New Zealand
- Karuna Sampath - University of Warwick, UK
- Kerstin Howe - Sanger Institute, Cambridge, UK
- Laura Clarke - EMBL-EBI, Cambridge, UK
- Leonie Kamminga - Radboud Institute for Molecular Life Sciences, Netherlands
- Sinnakaruppan Mathavan - Genome Institute of Singapore, China
- Monte Westerfield - University of Oregon, US
- Matt Clark - The Genome Analysis Centre, Norwich, UK
- Michael Hoffman - Department of Computer Science, University of Toronto
- Nadine Vastenhouw - Max Planc Institute, Germany
- Peter Alestrom - AzLab, Norwegian University of Life Sciences
- Piero Carninci - Riken, Japan
- Remo Sanges - Stazione Zoologica, Italy
- Robert Geisler - Karlsruhe Institute of Technology, Germany
- Shawn Burgess - National Human Research Genome Insitute, US
- Sridhar Sivasubbu - Institute of Genomics and Intetgrative Biology, New Delhi
- Tatjana Sauka Spengler - Radcliff Dept of Medicine, Oxford, UK
- Yi Zhou - Zon Laboratory, Harvard, US
DANIO-CODE WIKI
DANIO-CODE WIKI
DANIO-CODE WIKI
This WIKI provides up-to-date information about the status of DANIO-CODE activities, guide documents and forum for discussion.
Newsgroup email address
By registering at the WIKI, members will access the DANIO-CODE email server and newsgroup with the danio-code@zfin.org address
DANIO-CODE Data Coordination Center
DANIO-CODE Data Coordination Center
DANIO-CODE Data Co-Ordination Centre
This DANIO-CODE user’s guide is intended to assist users in the upload of zebrafish genomic data in order to create the largest collection of genomic/epigenomic/transcriptomic data with a thorough annotation of the origins and treatment of samples. These samples and annotation will allow for unprecedented, integrative analyses. We thank in advance the data producers for the upload and annotation of their data for the benefit of the research community!
The DCC core team are:
Previous meetings and events
Previous meetings and events
Data Annotation Jamboree, University of Liege, Belgium, 6th May 2016
Video recordings of Data Annotation Jamboree 6th May 2016
- DANIO-CODE DCC Upload Tutorial by Matthias Hörtenhuber
- Sequence Conservation Analysis by ANCORA by Boris Lenhard
- Considerations for the Integration of Zebrafish Gene Expression Database with Genomics Datasets by Dunja Vucenovic
- Danio-Code in the light of modENCODE by Ben Brown
- Considerations for the publication of the first DANIO-CDE by Carsten Daub
- Towards a first publication of a DANIO-CODE by Ferenc Mueller
- Introduction of the DANIO-CODE Data Coordination Centre by Carsten Daub
- DanioPeaks: Computational analysis Resource for DANIO-CODE by Boris Lenhard
- Introduction to the International Consortium Effort, DANIO-CODE by Ferenc Mueller
Consortium Formation Meeting - Imperial College London, December 2014
What was discussed...
- Annotation technologies
- Data processing and sharing
- Visualization
- Networking
- Consortium organisation
- Execution and tasks
- Publicity
What was agreed
Level I
- Generation of a track hub linked to browsers (end of 2015)
- all published data zebrafish genomics / epigenomics
- without quality filtering and for immediate access.
Level II
- Filter and reanalyze the available datasets (2016)
- new biological observations of publishable quality.
- a major multi-centre genomics paper
Level III
- To share unpublished data (future is bright)
- coordinated generation of new datasets
- scale up
Register with us
Register with us
Professor Ferenc Mueller - Coordinator
Professor of Developmental Genetics
Department of Cancer and Genomic Sciences
College of Medicine and Health
Edgbaston
Birmingham
B15 2TT
UK
Tel: +44 (0)121 414 2895
Email: f.mueller@bham.ac.uk
Dr Fiona Wardle - Coordinator
Randall Centre of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Email: fiona.wardle@kcl.ac.uk
Professor Carsten Daub - Data Coordination Centre Coordinator
Karolinska Insitutet Department of Biosciences and Nutrition (BioNut), H2Novum, SE-141 83 Hudding, Sweden
Email: carsten.daub@ki.se
Matthias Hörtenhuber - DCC data upload contact
Email: matthias.hortenhuber@ki.se
Marcus Stoiber - DCC data upload contact
Email: marcus.stoiber@gmail.com
Monte Westerfield - ZFIN, Track hub host
Email: monte.westerfield@gmail.com
Shelley Jukes - DANIO-CODE website enquiries
Email: s.jukes@bham.ac.uk
