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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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Citation and License

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

Published: 19 April 2009

Abstract

EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types and search patterns. The FANTOM4 EdgeExpress database http://fantom.gsc.riken.jp/4/edgeexpress webcite summarizes gene expression patterns in the context of alternative promoter structures and regulatory transcription factors and microRNAs using intuitive gene-centric and sub-network views. This is an important resource for gene regulation in acute myeloid leukemia, monocyte/macrophage differentiation and human transcriptional networks.