Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Database

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

Nodin Weddington, Alexander Stuy, Ichiro Hiratani, Tyrone Ryba, Tomoki Yokochi and David M Gilbert*

Author Affiliations

Department of Biological Sciences, Florida State University, Tallahassee, Florida 32306, USA

For all author emails, please log on.

BMC Bioinformatics 2008, 9:530  doi:10.1186/1471-2105-9-530

Published: 10 December 2008

Abstract

Background

Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property of specific cell types.

Results

We have developed ReplicationDomain http://www.replicationdomain.org webcite as a web-based database for analysis of genome-wide replication timing maps (replication profiles) from various cell lines and species. This database also provides comparative information of transcriptional expression and is configured to display any genome-wide property (for instance, ChIP-Chip or ChIP-Seq data) via an interactive web interface. Our published microarray data sets are publicly available. Users may graphically display these data sets for a selected genomic region and download the data displayed as text files, or alternatively, download complete genome-wide data sets. Furthermore, we have implemented a user registration system that allows registered users to upload their own data sets. Upon uploading, registered users may choose to: (1) view their data sets privately without sharing; (2) share with other registered users; or (3) make their published or "in press" data sets publicly available, which can fulfill journal and funding agencies' requirements for data sharing.

Conclusion

ReplicationDomain is a novel and powerful tool to facilitate the comparative visualization of replication timing in various cell types as well as other genome-wide chromatin features and is considerably faster and more convenient than existing browsers when viewing multi-megabase segments of chromosomes. Furthermore, the data upload function with the option of private viewing or sharing of data sets between registered users should be a valuable resource for the scientific community.