The Encyclopedia of DNA elements (ENCODE): data portal update

By Carrie A. Davis, B. Hitz, C. A. Sloan, Esther T. Chan, Jean M. Davidson, I. Gabdank, J. Hilton, K. Jain, Ulugbek K. Baymuradov, Aditi K. Narayanan and 8 more. Nucleic Acids Res., 2017

1,543 citations recorded by the source corpus.

Abstract The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/06f6cdcada5899bfef0a1151ae0cd19b9c43250c

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Citations in the corpus

EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species (2019, methodology): “We manually downloaded 16 055 datasets, including processed or the raw sequencing data, from NCBI GEO datasets (36), ENCODE project portal at UCSC (32), Epigenome Roadmap (7) and FANTOM5 (2).”
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal (2019, methodology): “All the experiments and their analyses on the ENCODE portal are represented using a structured metadata model that informs the interpretation of data in biological terms (3,4,6,32).”
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding (2022, methodology): “To construct the rankings based on our inferred peak–gene interactions, we first overlapped the ENCODE TF chromatin immunoprecipitation (ChIP) peaks 77 with the ATAC peaks and counted the number of ChIP peaks for each TF in each ATAC peak.”
The Cellosaurus, a Cell-Line Knowledge Resource. (2018, background): “org).(43) Currently, it has 5400 cell line “biosamples” that map back to;450 different cell lines.”
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis (2021, background): “…per-cell data quality, ArchR computes transcription start site (TSS) enrichment scores, which have become the standard for bulk ATAC-seq analysis 20 and provide clearer separation of cells generating low-and high-quality data compared to that from the fraction of reads in promoters 11…”
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis (2018, background): “Examples of new factors include ZBTB48 (35,36) and ZMYM3 (37) in human, and SPEN and TERF2IP (38) in mouse; and examples of new histone modifications / variants include H3F3A (37) and H2AFZ (37) in human, and H3K9BHB (39) and H2BK5me1 (40) in mouse (Figure 2D).”
A draft human pangenome reference (2022, background): “, 2014) and the ENCODE project (ENCSR000AED, replicate 1) (Davis et al., 2018; ENCODE Project Consortium, 2012).”