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ReplicationDomain (alias ChromosomeDomain)


NAR Molecular Biology Database Collection entry number 1292
Weddington, N., Stuy, A., Hiratani, I., Ryba, T., Yokochi, T., and Gilbert, D.M.
Florida State University, Tallahassee, FL, USA

Database Description

Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals). These replication domains replicate in a stable, cell type-specific temporal order during S-phase that is closely linked to their 3 dimensional organization in the nucleus and the expression of genes within each replication domain (Hiratani et al., Genome Res, 2010). ReplicationDomain is a database customized for analysis of genome-wide replication timing maps (replication profiles) from various cell lines and species and comparison to other genome-wide properties of chromosomes, such as transcription and chromatin immunoprecipitation data, which can also be uploaded and viewed (Weddington et al., BMC Bioinformatics, 2008). 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. ReplicationDomain is considerably faster and more convenient than existing browsers when viewing multi-megabase segments of chromosomes. 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 their data sets with any subset of the sites registered users; or (3) make their published or “in press” data sets publicly available.

Recent Developments

Since our last update (Nov., 2011), we have improved the ability of users to set up projects to recall and display specific datasets. At users request, we have added new pages for the Chicken, Arabadopsis and S. pombe genome to make a total of 6 species and over 330 datasets. New security features have been added, and gene aliases have been updated for all species. We have added the option for users to add the names of thier private datasets to a list of "requestable" datasets to promote interaction with other interested users. Finally, we have added several new tools to handle datasets from different genome builds.

Acknowledgements

This database is supported by NIH grant GM83337 and GM085354

References

1. Weddington, N., Stuy, A., Hiratani, I. Ryba, T., Yokochi, T. and Gilbert, D.M. (2008) ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data. BMC Bioinformatics, 9:530 (PMC2636809)
2. Hiratani, I., Ryba, T., Itoh, M., Rathjen, J., Kulik, M., Papp, B., Fussner, E., Bazett-Jones, D.P., Plath, K., Dalton, S., Rathjen, P.D., Gilbert, D.M. (2010) Genome-Wide Dynamics of Replication Timing Revealed by In Vitro Models of Mouse Embryogenesis, GENOME RESEARCH, 20:155-169 (PMC2813472)
3. Ryba, T., Battaglia, D., Pope, B.D., Hiratani, I. and Gilbert, D.M. (2011) Genome-Scale Analysis of Replication Timing: from Bench to Bioinformatics. NATURE PROTOCOLS 6:870-895 (PMC3111951)


DOI:10.1186/1471-2105-9-530
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