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

Weddington N, Stuy A, Hiratani I, Ryba T, Yokochi T, Gilbert DM - BMC Bioinformatics (2008)

Bottom Line: Furthermore, we have implemented a user registration system that allows registered users to upload their own data sets.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, Florida State University, Tallahassee, Florida 32306, USA. weddington@bio.fsu.edu

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 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.

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Data Display Page: An Exemplary View of A Region of Chromosome 8. Buttons correspond to descriptions in the text.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2636809&req=5

Figure 3: Data Display Page: An Exemplary View of A Region of Chromosome 8. Buttons correspond to descriptions in the text.

Mentions: In the near future, species other than the mouse (Mus musculus) will be available and the user will need to first choose a species and be redirected to the data available for that species, similar to the UCSC Genome Browser. At present, only mouse data are uploaded so the viewer opens to the mouse page directly. From the Main Page (Figure 1), you can jump to the Data Display page (Figure 3) and view your favorite chromosomal region in one of three ways:


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

Weddington N, Stuy A, Hiratani I, Ryba T, Yokochi T, Gilbert DM - BMC Bioinformatics (2008)

Data Display Page: An Exemplary View of A Region of Chromosome 8. Buttons correspond to descriptions in the text.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2636809&req=5

Figure 3: Data Display Page: An Exemplary View of A Region of Chromosome 8. Buttons correspond to descriptions in the text.
Mentions: In the near future, species other than the mouse (Mus musculus) will be available and the user will need to first choose a species and be redirected to the data available for that species, similar to the UCSC Genome Browser. At present, only mouse data are uploaded so the viewer opens to the mouse page directly. From the Main Page (Figure 1), you can jump to the Data Display page (Figure 3) and view your favorite chromosomal region in one of three ways:

Bottom Line: Furthermore, we have implemented a user registration system that allows registered users to upload their own data sets.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, Florida State University, Tallahassee, Florida 32306, USA. weddington@bio.fsu.edu

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 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.

Show MeSH