Category Archives: Regulation

Variants in regulatory regions

Posted on January 24, 2013 by Anja (Variation)

From release 70 we store and display information on the type of consequence a variant has on overlapping regulatory regions (Ensembl regulatory features and Ensembl motif features) for human and mouse. Web display One of the major benefits of this is that we … Continue reading →

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ENCODE integrative analysis data available in Ensembl

Posted on October 8, 2012 by Steve Searle

We are pleased to announce that we are now providing access to the ENCODE integrative analysis data from within Ensembl. These analyses bring together a multitude of experiments targeted at determining functional elements in the human genome sequence. This data … Continue reading →

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Human Methylation data in Ensembl

Posted on October 3, 2011 by Daniel (Regulation)

DNA methylation is an epigenetic mark known to be important in many biological processes, namely in the regulation of gene expression. In addition to MeDIP-Chip methylation datasets for 17 cell lines and tissues from Rakyan et al (2008), Ensembl now also … Continue reading →

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Transcription Factor Binding Sites in Ensembl

Posted on May 18, 2011 by Daniel (Regulation)

Ensembl provides annotations indicating regions in the genome that are experimentally verified to be bound by transcription factors (from ChIP-Seq experiments). Within these regions, we now also provide precise transcription factor binding sites. To generate these binding sites, we make use … Continue reading →

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Web display speed ups and flat file usage

Posted on May 3, 2011 by Nathan (Regulation)

We’re always looking at ways we can improve the Ensembl browser experience.  Quite often this results in a focus on the speed at which a particular display or track can be provided.  Over the past year or so we have … Continue reading →

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243 ENCODE ChIP-Seq Experiments

Posted on April 5, 2011 by Giulietta (Outreach)

The ENCODE project is generating an immense amount of data.  ChIP-Seq, ChIP-ChIP, and RNA-Seq experiments are yielding an exciting number of sequences that may be involved in gene regulation.  Trying to look at these data individually would be a lot … Continue reading →

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Regulatory Build now Cell Type specific

Posted on August 16, 2010 by Daniel (Regulation)

Since release 58, the Ensembl Regulatory Build has been cell type specific. Regulatory Features are defined as sites of open chromatin which are potentially involved in gene regulation. These are built using data from different cell types, resulting in differing … Continue reading →

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New ChIP-Seq data and visualisation

Posted on August 13, 2010 by Nathan (Regulation)

Over the last 3 releases we have significantly increased the content of the functional genomics databases, by including data from large public projects such as ENCODE and The Epigenomics Roadmap. In release 59 we have over 200 human data sets … Continue reading →

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The eFG Array Mapping Environment

Posted on May 5, 2009 by Nathan (Regulation)

The Ensembl Functional Genomics (eFG) environment has been expanded to incorporate array mapping functionality. Historically, arrays from different vendors have been processed in similar, but non-identical ways due to differing array designs, with the output being stored in the core … Continue reading →

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