The Human Epigenome Browser at Washington University

Motivation: Multiple high-throughput approaches have recently been developed and allowed the discovery of enhancers on a genome scale in a single experiment. However, the datasets generated from these approaches are not fully utilized by the research community due to technical challenges such as lack of consensus enhancer annotation and integrative analytic tools. Results: We developed an interactive database, EnhancerAtlas, which contains an atlas of 2,534,123 enhancers for 105 cell/tissue types. A consensus enhancer annotation was obtained for each cell by summation of independent experimental datasets with the relative weights derived from a cross-validation approach. Moreover, EnhancerAtlas provides a set of useful analytic tools that allow users to query and compare enhancers in a particular genomic region or associated with a gene of interest, and assign enhancers and their target genes from a custom dataset. Availability and Implementation: The database with analytic tools is available at http://www.enhan ceratlas.org/.

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“…6A). We also provide a link to the Epigenome browser (Zhou et al, 2011) for an alternative display. (B) Search enhancers by gene name.…”

Section: Web Servermentioning

confidence: 99%

EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types

et al. 2016

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“…Further analysis was performed using SeqMonk (http:// www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and the data were visualized using the WashU Epigenome browser. 25 …”

Section: Hi-c With Sequence Capture Enrichmentmentioning

confidence: 99%

Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model

Wilson

Schoenfelder

Hannah

et al. 2016

Blood

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“…Beginning in 2010, the Roadmap program invested targeted resources in a new generation of visualization tools designed to facilitate the display and manipulation of large numbers of data tracks. As a result, a variety of novel interfaces are now becoming available such as the epigenome visualization hub (Zhou et al 2011). In addition, new types of data exploration tools are being developed which will enable pattern-based exploration of ENCODE or Roadmap data sets.…”

Section: Seeing the Big Picturementioning

confidence: 99%

What does our genome encode?

Stamatoyannopoulos

2012

Genome Res.

107

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In its first production phase, The ENCODE Project Consortium (ENCODE) has generated thousands of genome-scale data sets, resulting in a genomic “parts list” that encompasses transcripts, sites of transcription factor binding, and other functional features that now number in the millions of distinct elements. These data are reshaping many long-held beliefs concerning the information content of the human and other complex genomes, including the very definition of the gene. Here I discuss and place in context many of the leading findings of ENCODE, as well as trends that are shaping the generation and interpretation of ENCODE data. Finally, I consider prospects for the future, including maximizing the accuracy, completeness, and utility of ENCODE data for the community.

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The Human Epigenome Browser at Washington University

Cited by 303 publications

References 5 publications

EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types

EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types

Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model

What does our genome encode?

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