Ensembl Funcgen Summary
Deprecation note
As of release 113, it is no longer recommended to access funcgen data via the Perl API or the funcgen DB. See Accessing regulatory data for alternative options.
If the Funcgen Perl API or database is important to your research, please let us know about your use case by emailing helpdesk@ensembl.org.
Database Description
The Ensembl regulation database and API are developed and maintained by the Ensembl Regulation team. The main focus of the 'funcgen' database is on experimental data which may elucidate transcriptional regulation. The schema was originally designed to support ChIP on Chip tiling array experiments but soon expanded to support other sequencing-based technologies. The original requirements supported use as a local data storage and analysis platform, as such the regulation data bases supports multiple coordinate systems. There is also support for micro array designs and externally curated data sets. See here for a summary of the data base content.
- Schema documentation: page describing every column of every table of the Ensembl Funcgen database schema.
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Database diagram : The Regulation Database schema is available below and is broken into several individual parts
Perl API
A comprehensive Perl Application Program Interface (API) provides efficient access to the Ensembl Funcgen database.
- API Installation: A step-by-step installation guide for all Perl Ensembl APIs.
- Funcgen API Documentation: A complete reference to the objects and methods used in the Funcgen database API, through the Doxygen tool.
- Funcgen API Tutorial: An introduction to the underlying concepts of the Funcgen database API.
Ensembl Software Support
Ensembl is an open project and we would like to encourage correspondence and discussions on any subject on any aspect of Ensembl. Please see the Ensembl Contacts page for suitable options getting in touch with us.