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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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Uploading Your Own Data Set. (A, B) Data file structures. Exemplary tab-delimited text data files for replication timing (A) and transcription (B). (C) A screenshot of the "Data Upload" page.
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Figure 5: Uploading Your Own Data Set. (A, B) Data file structures. Exemplary tab-delimited text data files for replication timing (A) and transcription (B). (C) A screenshot of the "Data Upload" page.

Mentions: To upload your data set, first generate a single, tab-delimited text file for each data set that includes the following 6 columns in this order as shown in Figures 5A and 5B: Gene/Probe ID (any unique identifier of genes or probes), Gene Name (type NA when unavailable), Chromosome, Chromosome Start, Chromosome End, and Data Value. You can also add a Present- Absent (P = 1, A = 0) column as a 7th column for transcription data sets. Then, log in with your ReplicationDomain account (Figure 1, button 5), go to the "Database" link from the main menu (Figure 1, button 1), click the "Upload data set" link and fill out the form (Figure 5C) with the requested attributes, select your text data file and hit "send." This should upload your data set, which will appear on the Data Display page for graphical display as well as on the list of data sets found under the "List my data sets" link on the Database page. All of the current 14 data set attributes are described under "Definitions of Data Entry Terms" below, which includes Data Security Level (description also on our Documentation page). Users can select Public, Private, or Über Private. Public data sets can be viewed by any user without a login requirement, but we require such data sets to be published or "in press" in peer-reviewed journals for database quality assurance purposes (i.e. a reference must be provided). Private data sets are viewable by all registered users with a ReplicationDomain account, while Über Private data sets are viewable only by the registered user who uploaded them. In the future, we anticipate implementing additional data security mechanisms that will allow sharing of data sets among designated registered users. Finally, existing data set attributes including Data Security Level can be edited later if necessary: click the "Database" link from the main menu, identify your data set from "List my data sets" link, hit "Edit," make necessary modifications, and hit "Update."


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)

Uploading Your Own Data Set. (A, B) Data file structures. Exemplary tab-delimited text data files for replication timing (A) and transcription (B). (C) A screenshot of the "Data Upload" page.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Uploading Your Own Data Set. (A, B) Data file structures. Exemplary tab-delimited text data files for replication timing (A) and transcription (B). (C) A screenshot of the "Data Upload" page.
Mentions: To upload your data set, first generate a single, tab-delimited text file for each data set that includes the following 6 columns in this order as shown in Figures 5A and 5B: Gene/Probe ID (any unique identifier of genes or probes), Gene Name (type NA when unavailable), Chromosome, Chromosome Start, Chromosome End, and Data Value. You can also add a Present- Absent (P = 1, A = 0) column as a 7th column for transcription data sets. Then, log in with your ReplicationDomain account (Figure 1, button 5), go to the "Database" link from the main menu (Figure 1, button 1), click the "Upload data set" link and fill out the form (Figure 5C) with the requested attributes, select your text data file and hit "send." This should upload your data set, which will appear on the Data Display page for graphical display as well as on the list of data sets found under the "List my data sets" link on the Database page. All of the current 14 data set attributes are described under "Definitions of Data Entry Terms" below, which includes Data Security Level (description also on our Documentation page). Users can select Public, Private, or Über Private. Public data sets can be viewed by any user without a login requirement, but we require such data sets to be published or "in press" in peer-reviewed journals for database quality assurance purposes (i.e. a reference must be provided). Private data sets are viewable by all registered users with a ReplicationDomain account, while Über Private data sets are viewable only by the registered user who uploaded them. In the future, we anticipate implementing additional data security mechanisms that will allow sharing of data sets among designated registered users. Finally, existing data set attributes including Data Security Level can be edited later if necessary: click the "Database" link from the main menu, identify your data set from "List my data sets" link, hit "Edit," make necessary modifications, and hit "Update."

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