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

doi:10.1186/gb-2009-10-4-r39

Genome Biology

Volume 10
Issue 4

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Severin J
Waterhouse AM
Kawaji H
Lassmann T
van Nimwegen E
Balwierz PJ
de Hoon MJ
Hume DA
Carninci P
Hayashizaki Y
Suzuki H
Daub CO
Forrest AR

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Severin J
Waterhouse AM
Kawaji H
Lassmann T
van Nimwegen E
Balwierz PJ
de Hoon MJ
Hume DA
Carninci P
Hayashizaki Y
Suzuki H
Daub CO
Forrest AR
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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 Forrest¹^,4

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

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

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

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

author email corresponding author email* Contributed equally

Genome Biology 2009, 10:R39doi:10.1186/gb-2009-10-4-r39


Published:	19 April 2009

Subject areas: Bioinformatics, Genome studies, Molecular biology

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.