MAPPER-2
Abbreviation:mapperdb
General Information
This resource provides information primarily on the upstream non-coding sequence data of genes in 3 genomes which gives insight into the transcription factors binding sites (TFBSs). For each transcript, the region scanned extends from 10,000bp upstream of the transcript start to 50bp downstream of the coding sequence start. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons.
Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs.
How to cite this record
FAIRsharing.org: mapperdb; MAPPER-2; DOI: https://doi.org/10.25504/FAIRsharing.1ex4pm;
Last edited: Feb. 22, 2018, 2:43 p.m.; Last accessed: Sep 23 2018 1:42 a.m.
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Edits to 'https://fairsharing.org/FAIRsharing.1ex4pm' by 'The FAIRsharing Team' at 13:52, 08 Sep 2016 (approved):
'name' has been modified:
Before: The MAPPER-2 database: A multi-genome catalog of putative transcription factor binding sites
After: MAPPER-2
Edits to 'https://fairsharing.org/FAIRsharing.1ex4pm' by 'The FAIRsharing Team' at 10:38, 06 Sep 2016 (approved):
'description' has been modified:
Before: Putative transcription factor binding sites in various genomes
After: This resource provides information primarily on the upstream non-coding sequence data of genes in 3 genomes which gives insight into the transcription factors binding sites (TFBSs).
Support
No support information provided.
Additional Information
Access / Retrieve Data
Conditions of Use
Data Versioning
| no versioning policy
|
No link recorded |
| access to historical files available
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No link recorded |
Data Release
| ad-hoc release
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No link recorded |
Data Curation
| automated annotation
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No link recorded |
Data Access
| web interface
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No link recorded |
| file download(tab-delimited)
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No link recorded |
| programatic interface (DB-RPC]
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No link recorded |
Publications
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.
Marinescu VD., Kohane IS., Riva A.,
BMC Bioinformatics 2005
View Paper (PubMed)
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.
Marinescu VD., Kohane IS., Riva A.,
Nucleic Acids Res. 2005
View Paper (PubMed)
Related Standards
Reporting Guidelines
No guidelines defined
Terminology Artifacts
No semantic standards defined
Related Databases
No related databases defined
Implementing Policies
This record is not implemented by any policy.
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