Open Access Highly Accessed Software

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 Forrest1,4*

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

For all author emails, please log on.

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.