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Ensembl Functional Genomics

Database Description

The Ensembl Funcgen database (eFG) database and API stores functional genomics experiments submitted to Ensembl from our collaborators. eFG is a dual purpose system which can be used as a normal ensembl database or as a local or laboratory data storage and analysis platform. Due to the differing requirements from nature of the data and duality of function, eFG is a multi-coordinate system database. The database includes:

  • Experimental data and meta data from functional genomics experiments using the following technologies:
    • Chromatin immunoprecipitation using tiling arrays (ChIP-chip)
    • Chromatin immunoprecipitation using 2nd generation sequencing (ChIP-Seq)
  • Experimental data on epigenomic modifications and DNA binding proteins:
    • Histone modifications
    • DNase1 Hypersensitivity sites
    • RNAPollII
    • CCCTC binding factor
  • Externally curated data with a regulatory focus:
    • cisRED - Regulatory motifs
    • miRanda - miRNA targets
    • VISTA - Enhancers
  • The Ensembl Regulatory Build - Regulatory features generated from a combined analysis of all of the above.

Database Schema

The table layout of the database is explained in the following document:

Perl API

A comprehensive Perl Application Programme Interface (API) provides efficient access to the Ensembl Compara database.

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.