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VISTA Enhancer Browser specifications

Information


Unique identifier OMICS_01568
Name VISTA Enhancer Browser
Restrictions to use None
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline VISTA Enhancer Browser

Publication for VISTA Enhancer Browser

VISTA Enhancer Browser citations

 (14)
library_books

An information theoretic approach to the modeling and analysis of whole genome bisulfite sequencing data

2018
BMC Bioinformatics
PMCID: 5842653
PMID: 29514626
DOI: 10.1186/s12859-018-2086-5

[…] aggregate differential GU classifications among all cancer/normal comparisons in terms of methylation level and entropy (Additional file : Figures S8 and S9). We obtained a list of enhancers from the VISTA enhancer browser [] by using all human (hg19) positive enhancers that show reproducible expression in at least three independent transgenic embryos. We defined promoter regions as sequences flan […]

library_books

A new method for enhancer prediction based on deep belief network

2017
BMC Bioinformatics
PMCID: 5657043
PMID: 29072144
DOI: 10.1186/s12859-017-1828-0

[…] ntifying enhancers using DNA sequence, transcription factor binding site motifs and other sequence patterns, it is publicly available as a web server. The DEEP method and EnhancerFinder work with the VISTA Enhancer Browser. To evaluate ChromHMM and Segway, we considered the states overlapping our training and testing regions. Any region with an overlapping enhancer state was considered an enhancer […]

library_books

An imprinted non coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

2017
PMCID: 5433149
PMID: 28506242
DOI: 10.1186/s13045-017-0465-4

[…] -referenced with the University of Tennessee CTCF binding site database, which includes data from the UCSC genome browser and the Broad Institute []. Search for enhancer sites was performed using the VISTA Enhancer Browser (Lawrence Berkeley National Laboratory) as previously described []. […]

library_books

Genome wide compendium and functional assessment of in vivo heart enhancers

2016
Nat Commun
PMCID: 5059478
PMID: 27703156
DOI: 10.1038/ncomms12923

[…] enes with relevant functions (). For example, 11 out of the 12 most enriched human phenotypes represent cardiovascular conditions (). In addition, 152 out of 170 (89%) heart enhancers reported in the VISTA Enhancer Browser, a large collection of in vivo enhancers validated in transgenic mice, are identified as candidate heart enhancers in the present catalogue (, , ). This high rediscovery rate hi […]

library_books

Distinct epigenetic signatures elucidate enhancer gene relationships that delineate CIMP and non CIMP colorectal cancers

2016
Oncotarget
PMCID: 5053707
PMID: 27049830
DOI: 10.18632/oncotarget.8473

[…] ions were discovered by methylKit to be differentially methylated between the CIMP and non-CIMP groups ().We compared these 16,092 DMRs against 1729 experimentally validated human gene enhancers from VISTA Enhancer Browser [] and found that 24 DMRs were found completely within 24 different gene enhancers.Of the 24 enhancers identified by methylKit to contain a DMR, we wanted to prioritize and narr […]

library_books

Progress and challenges in bioinformatics approaches for enhancer identification

2015
Brief Bioinform
PMCID: 5142011
PMID: 26634919
DOI: 10.1093/bib/bbv101

[…] s (e.g. scrambled enhancers). However, with the recent advances on computational and experimental techniques, the ENCODE integrative annotation [], the Atlas of actively transcribed enhancers [], the VISTA enhancer browser [] and the outcome of individual studies based on enhancer-screening data (similar to those we summarized before) can serve as baseline sources for implementing more reliable ML […]


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VISTA Enhancer Browser institution(s)
Genomics Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA; US Department of Energy Joint Genome Institute, Walnut Creek CA, USA

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