ENCODE data at the ENCODE portal

By C. A. Sloan, Esther T. Chan, Jean M. Davidson, V. Malladi, J. Strattan, B. Hitz, I. Gabdank, Aditi K. Narayanan, Marcus Ho, Brian T. Lee and 7 more. Nucleic Acids Res., 2015

522 citations recorded by the source corpus.

The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase of creating a comprehensive catalog of functional elements in the human genome. This phase of the project includes an expansion of assays that measure diverse RNA populations, identify proteins that interact with RNA and DNA, probe regions of DNA hypersensitivity, and measure levels of DNA methylation in a wide range of cell and tissue types to identify putative regulatory elements. To date, results for almost 5000 experiments have been released for use by the scientific community. These data are available for searching, visualization and download at the new ENCODE Portal (www.encodeproject.org). The revamped ENCODE Portal provides new ways to browse and search the ENCODE data based on the metadata that describe the assays as well as summaries of the assays that focus on data provenance. In addition, it is a flexible platform that allows integration of genomic data from multiple projects. The portal experience was designed to improve access to ENCODE data by relying on metadata that allow reusability and reproducibility of the experiments.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5606cae9b1e1189b816d198d8793dd079b53fc67

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient (2017, unknown): “Weobtainedthe Hi-C data of 11 human cancercelllines from the ENCODE data portal (Sloan et al. 2016) (https://www. encodeproject.org/matrix/?type=Experiment&status=released& assay_slims=3D+chromatin+structure&award.project=ENCODE& assay_title=Hi-C).”
The UCSC Genome Browser database: 2017 update (2016, unknown): “org) (34) hosted by Stanford University.”
Variation Interpretation Predictors: Principles, Types, Performance, and Choice (2016, background): “The Encyclopedia of DNA Elements (ENCODE) project [Sloan et al., 2016] aims at identifying and mapping functional and regulatory elements in the human genome also outside protein coding regions.”
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update (2016, methodology): “…associated with grants us-ing NIH RePORTER and GeneRIF (22); transcription factor targets computed from the ChIP-seq data from the EN-CODE project (23); differentially expressed genes from the Allen Brain Atlas (24); tissue expression extracted from the Genotype-Tissue Expression (GTEx) project…”
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).”
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability (2016, background): “…a prioritized set of various cell types to complete annotations about genes and their RNA transcripts and transcriptional regulatory regions and have developed data standards that utilizes the CL, among other ontologies, to describe the metadata for cell types used and experimental assays [60, 61].”
The UCSC Genome Browser database: 2019 update (2018, background): “Examples include cis-regulatory annotations created by JASPAR (3), ReMap (4), the Eukaryotic Promoter Database (5), ENCODE(6), the Ensembl regulatory build (7) and Brain and Roadmap Epigenomics (8), RNAs from FANTOM5 (9), Mouse Alleles from MGI (10), lncRNAs from LNCipedia (11), Cancer genomics (sho”
Transcriptomics technologies (2017, methodology): “The current benchmarks recommended by the Encyclopedia of DNA Elements (ENCODE) Project are for 70-fold exome coverage for standard RNA-Seq and up to 500-fold exome coverage to detect rare transcripts and isoforms [81][82][83].”