The ENCODEdb portal: Simplified access to ENCODE Consortium data

Abstract

The Encyclopedia of DNA Elements (ENCODE) project aims to identify and characterize all functional elements in a representative chromosomal sample comprising 1% of the human genome. Data generated by members of The ENCODE Project Consortium are housed in a number of public databases, such as the UCSC Genome Browser, NCBI's Gene Expression Omnibus (GEO), and EBI's ArrayExpress. As such, it is often difficult for biologists to gather all of the ENCODE data from a particular genomic region of interest and integrate them with relevant information found in other public databases. The ENCODEdb portal was developed to address this problem. ENCODEdb provides a unified, single point-of-access to data generated by the ENCODE Consortium, as well as to data from other source databases that lie within ENCODE regions; this provides the user a complete view of all known data in a particular region of interest. ENCODEdb Genomic Context searches allow for the retrieval of information on functional elements annotated within ENCODE regions, including mRNA, EST, and STS sequences; single nucleotide polymorphisms, and UniGene clusters. Information is also retrieved from GEO, OMIM, and major genome sequence browsers. ENCODEdb Consortium Data searches allow users to perform compound queries on array-based ENCODE data available both from GEO and from the UCSC Genome Browser. Results are retrieved from a specific genomic area of interest and can be further manipulated in a variety of contexts, including the UCSC Genome Browser and the Galaxy large-scale genome analysis platform. The ENCODEdb portal is freely accessible at http://research. nhgri.nih.gov/ENCODEdb.

Solutions for biomedical grid computing—Case studies from the D-Grid project Services@MediGRID

“…Both are front-ends of their own dedicated data management centers, attempt to be hotspots for data analysis and in the latter case also serve as visualization service for other data centers as, e.g. ENCODE [57]. Although these browsers have been beneficial in the understanding of the complex organization of genomes, there are also limitations concerning their focus on linear presentation, standardized input and data bank accessibility.…”

Identification and Computational Analysis of Gene Regulatory Elements

“…Primary data from ENCODE are available at the NCBI GEO (http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html) and the EBI ArrayExpress (http://www.ebi.ac.uk/arrayexpress/) public array data repositories. The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE), the ENCODE resource page at Ensembl (http://www.ensembl.org/Homo_sapiens/encode.html), and the ENCODEdb portal at NHGRI (http://research.nhgri.nih.gov/ENCODEdbGRI) provide convenient links for access (Elnitski et al 2007; Rosenbloom et al 2010). Unreleased data can be viewed on the UCSC Preview Browser (http://genome-preview.ucsc.edu/).…”

linc00673 (ERRLR01) is a prognostic indicator of overall survival in breast cancer

“…The ENCODE Consortium determined the abundance and genomic location of many lncRNAs across several species, which in various cases are conserved through positional synteny. 8,9 LncRNAs reside near protein coding regions and function in cis to maintain the surrounding chromatin in an open and epigenetically active state. In other cases, lncRNAs are transcribed in an anti-sense orientation to a protein-coding gene, which in turn recruits histone chromatin-modifying complexes that support gene silencing.…”