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FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

Jessica Severin1*, Andrew M Waterhouse1, Hideya Kawaji1, Timo Lassmann1, Erik van Nimwegen2, Piotr J Balwierz2, Michiel JL de Hoon1, David A Hume3, Piero Carninci1, Yoshihide Hayashizaki1, Harukazu Suzuki1, Carsten O Daub1 and Alistair RR Forrest14*

Author Affiliations

1 RIKEN Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan

2 Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse, CH-4056 Basel, 4056, Switzerland

3 The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Roslin, EH259PS, UK

4 The Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane Innovation Park, Don Young Road, Nathan, QLD 4111, Australia

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Genome Biology 2009, 10:R39  doi:10.1186/gb-2009-10-4-r39

Published: 19 April 2009

Additional files

Additional File 1:

Summary of the current data stored in EEDB at the time of publication, and the accession numbers for each of the raw data sets (from CIBEX and DDBJ).

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Additional File 2:

The EGR1 gene as an example in the gene centric view of EEDB.

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Additional File 3:

The sub-network view of EEDB.

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Additional File 4:

Information available as popups in EEDB (edge types and edge weights used in EEDB, CAGE defined promoters, and an explanation of the subnet view).

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Open Data

Additional File 5:

An example of how EEDB can be used with gene-centric and sub-network views for the key monocytic marker CD14.

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Open Data