ENCODE whole-genome data in the UCSC Genome Browser: update 2012
By Kate R. Rosenbloom, Timothy R. Dreszer, J. Long, V. Malladi, C. A. Sloan, Brian J. Raney, Melissa S. Cline, Donna Karolchik, Galt P. Barber, Hiram Clawson and 17 more. Nucleic Acids Res., 2011
304 citations recorded by the source corpus.
The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human genome. The past year has brought the ENCODE compendium of functional elements to critical mass, with a diverse set of 27 biochemical assays now covering 200 distinct human cell types. Within the mouse genome, which has been under study by ENCODE groups for the past 2 years, 37 cell types have been assayed. Over 2000 individual experiments have been completed and submitted to the Data Coordination Center for public use. UCSC makes this data available on the quality-reviewed public Genome Browser (http://genome.ucsc.edu) and on an early-access Preview Browser (http://genome-preview.ucsc.edu). Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal (http://encodeproject.org) provides specialized tools and information about the ENCODE data sets.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/0344ac25ea2e9834b712d42109e9a1251005c666
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
- Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool (2013, methodology): “These six libraries include the ability to identify transcription factors that are enriched for target genes within the input list using four different options: 1) ChEA [10]; 2) position weight matrices (PWMs) from TRANSFAC [11] and JASPAR [12]; 3) target genes generated from PMWs downloaded from th”
- The Encyclopedia of DNA elements (ENCODE): data portal update (2017, methodology): “This corpus of data provides an astounding resource for annotation, curation and functional characterization in the human and mouse genomes in a large variety of sample types (2,3).”