CollecTF

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Link/URL:	http://collectf.umbc.edu
What:	CollecTFcompiles data on experimentally validated, naturally occurring TF-binding sites across the Bacteria domain, placing a strong emphasis on the transparency of the curation process, the quality and availability of the stored data and fully customizable access to its records.
Who:	CollecTF is developed and maintained by the Erill Lab at UMBC, in collaboration with the NCBI RefSeq database.
Updates:	CollecTF is under continuous revision, operating on a dual curation process that combines in-house curation by undergraduate students and direct submissions by authors.
Upcoming events:	CollecTF can be leveraged for team-based, active learning activities in Genetics and Biochemistry courses. Please email the collecTF team for further information.
Web Services:	Data in CollecTF is preiodically pushed to NCBI RefSeq complete genomes
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About CollecTF

CollecTF compiles data on experimentally validated, naturally occurring TF-binding sites across the Bacteria domain, placing a strong emphasis on the transparency of the curation process, the quality and availability of the stored data and fully customizable access to its records. CollecTF integrates multiple sources of data automatically and openly, allowing users to dynamically redefine binding motifs and their experimental support base. Most importantly, CollecTF entries are periodically submitted to NCBI for integration into RefSeq complete genome records as db_xref link-out features embedded in genome annotations. Experimentally-validated binding sites for transcription factors are therefore embedded in genome annotations as bound_moiety tags, providing information on the available experimental evidence, its published sources and a link to the full curation record on CollecTF. This approach maximizes the visibility of transcriptional regulation data by enriching the annotation of RefSeq files with regulatory information, addressing a decades-old deficit in the NCBI annotation pipeline. Hence, CollecTF operates both as a standalone database and as an open portal for entering of regulatory information into RefSeq genomes, generating a sustainable model that encourages direct author submissions in combination with in-house validation and curation of published literature.

Content

CollecTF uses exclusively a single data source: published experimental evidence on TFBS. Sites may be supported by evidence of binding and/or evidence of their regulation of gene expression. In silico evidence is also collected, but only as complement to experimental evidence. CollecTF defines three site types: motif associated, variable motif associated and non-motif associated, based on the availability of known binding patterns associated with reported sites.

Using CollecTF

Browsing

CollecTF can be browsed at three different levels

NCBI Taxonomy - Browse the database using up-to-date NCBI taxonomy. Just click on each taxonomical unit to expand it and see its associated information, and link out to species-specific reports.

TF family - Browse the database by transcription factor families. Click on each family to expand it and see its associated information, and link out to TF-family or TF-based reports.

Technique - Browse CollecTF by experimental evidence. Click on different groups of experimental techniques to expand them and see their associated information, and link out to technique.

Usage examples

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References

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External Links

[link CollecTF] URL:link