Gene Expression Data on ENSEMBL

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Ensembl Regulation provides resources used for studying gene expression and its regulation in human and mouse, with a focus on the transcriptional and post-transcriptional mechanisms. Our database includes the Ensembl Regulatory Build, an up-to-date and comprehensive summary of regulatory features across the genome, as well as popular curated external resources.


Gene expression is controlled by a complicated network of transcription factors and repressors, interacting with genomic features such as promoters and enhancers, dependant on epigenetic marks at those loci. Ensembl provides access to epigenomic data on histone modifications and protein binding across the genome, integrated with data on genes and genetic variation.

Join Ensembl to investigate a genomic region which controls gene expression, determine its activity in different cell types and view the epigenomic markers at that locus, plus see how to access these data in bulk.


Regulatory features

Regions that are predicted to regulate gene expression are called Regulatory features in Ensembl. The different types of regulatory features annotated include:

  • Promoters (regions at the 5' end of genes where transcription factors and RNA polymerase bind to initiate transcription)

  • Promoter flanking regions (transcription factor binding regions that flank the above)

  • Enhancers (regions that bind transcription factors and interact with promoters to stimulate transcription of distant genes)

  • CTCF binding sites (regions that bind CTCF, the insulator protein that demarcates open and closed chromatin)

  • Transcription factor binding sites (sites which bind transcription factors, for which no other role can be determined as yet)

  • Open chromatin regions (regions of spaced out histones, making them accessible to protein interactions)

       For each cell type the regulatory features are assigned labels to describe their activity levels. These include:

  • ACTIVE, when the feature displays an active epigenetic signature.

  • POISED, when the feature displays a epigenetic signature with the potential to be activated.

  • REPRESSED, when the feature is epigenetically repressed.

  • INACTIVE, when the region bears no epigenetic modifications from the ones included in the Regulatory Build.

  • NA, when there is no available data in the cell type for this feature.


       The Ensembl Regulatory Build (Zerbino et al. 2015) contains a genome-wide set of regions that are likely to be involved in gene regulation. The classification of these regions are:

  • Promoters

  • Promoter flanking regions

  • Enhancers

  • CTCF binding sites

  • Transcription factor binding sites

  • Open chromatin regions

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