ENCODE Data in the UCSC Genome Browser: year 5 update

By Kate R. Rosenbloom, C. A. Sloan, V. Malladi, Timothy R. Dreszer, Katrina Learned, V. Kirkup, M. Wong, M. Maddren, Ruihua Fang, Steven G. Heitner and 11 more. Nucleic Acids Res., 2012

814 citations recorded by the source corpus.

The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome, and its third year of investigations in the mouse genome. Since the last report in this journal, the ENCODE human data repertoire has grown by 898 new experiments (totaling 2886), accompanied by a major integrative analysis. In the mouse genome, results from 404 new experiments became available this year, increasing the total to 583, collected during the course of the project. The University of California, Santa Cruz, makes this data available on the public Genome Browser http://genome.ucsc.edu for visual browsing and data mining. Download of raw and processed data files are all supported. The ENCODE portal provides specialized tools and information about the ENCODE data sets.

Subfields: Molecular Biology

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Citations in the corpus

The UCSC Genome Browser database: 2017 update (2016, methodology): “The UCSC Genome Browser offers ENCODE data through 2012 (33).”
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data (2015, background): “Projects such as ENCODE (Rosenbloom et al. , 2013) or BLUEPRINT (Adams et al. , 2012) generated terabytes of sequencing data, providing new insights into the molecular mechanisms of the cell.”
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome (2020, methodology): “For TFBS prediction, we retrieved the ENCODE 690 ChIP-seq profiles from UCSC genome browser that covers 161 TFs in 91 human cell lines (37,38) (http://hgdownload.”
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data (2019, methodology): “The chromatin states for K562, GM12878, and HUVEC are downloaded from the ENCODE project at UCSC [46] (Additional file 1).”
CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences (2014, neutral): “Further investigation of these two sites using the ENCODE annotation from UCSC genome browser (36,37) revealed that R-30 Off-4, which had high off-target activity, targeted a site within 400 bp of the 3′ end of a long non-coding RNA (RP4-756H11.”
The UCSC Genome Browser database: 2015 update (2014, methodology): “With the completion of UCSC’s Data Coordination Center responsibilities for ENCODE, the ENCODE portal (en-codeproject.org) was migrated to the new ENCODE DCC.”
The UCSC Genome Browser database: 2014 update (2013, methodology): “During the transition of the ENCODE Data Coordination Center role to a joint collaboration with Stanford University, the Genome Browser team has continued to add signiﬁcant new content to the ENCODE data portal (http://encodeproject.org) and publish newly reprocessed ENCODE data sets (10).”
The UCSC Genome Browser database: 2019 update (2018, methodology): “For ChIP-Seq peaks of the ENCODE project we introduced the narrowPeak format, a BED-like custom track text file format that stores the signal peak, its summit, the P-value and the q-value (24).”
Ensembl 2014 (2013, methodology): “For example, the data produced by the ENCODE consortium (8) can be viewed by loading the ENCODE track hub (9) and users can then access an experiment matrix within the”
Gene regulation by the act of long non-coding RNA transcription (2013, background): “These studies have been made easier in the mouse and human genome due to the publicly available ENCODE data [127].”
Chromatin-state discovery and genome annotation with ChromHMM (2017, methodology): “Such information for a number of additional assemblies is available from the UCSC Genome Browser 73 .”