title: The ENCODE Project at UC Santa Cruz.
abstract: The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development of new methods to rigorously analyze a defined 1% of the human genome sequence. Experimental datasets are focused on the origin of replication, DNase I hypersensitivity, chromatin immunoprecipitation, promoter function, gene structure, pseudogenes, non-protein-coding RNAs, transcribed RNAs, multiple sequence alignment and evolutionarily constrained elements. The ENCODE project at UCSC website (http://genome.ucsc.edu/ENCODE) is the primary portal for the sequence-based data produced as part of the ENCODE project. In the pilot phase of the project, over 30 labs provided experimental results for a total of 56 browser tracks supported by 385 database tables. The site provides researchers with a number of tools that allow them to visualize and analyze the data as well as download data for local analyses. This paper describes the portal to the data, highlights the data that has been made available, and presents the tools that have been developed within the ENCODE project. Access to the data and types of interactive analysis that are possible are illustrated through supplemental examples.
authors.affiliation: Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA. daryl@soe.ucsc.edu
authors.forename: Daryl J
authors.initials: DJ
authors.lastname: Thomas
authors.forename: Kate R
authors.initials: KR
authors.lastname: Rosenbloom
authors.forename: Hiram
authors.initials: H
authors.lastname: Clawson
authors.forename: Angie S
authors.initials: AS
authors.lastname: Hinrichs
authors.forename: Heather
authors.initials: H
authors.lastname: Trumbower
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Raney
authors.forename: Donna
authors.initials: D
authors.lastname: Karolchik
authors.forename: Galt P
authors.initials: GP
authors.lastname: Barber
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Harte
authors.forename: Jennifer
authors.initials: J
authors.lastname: Hillman-Jackson
authors.forename: Robert M
authors.initials: RM
authors.lastname: Kuhn
authors.forename: Brooke L
authors.initials: BL
authors.lastname: Rhead
authors.forename: Kayla E
authors.initials: KE
authors.lastname: Smith
authors.forename: Archana
authors.initials: A
authors.lastname: Thakkapallayil
authors.forename: Ann S
authors.initials: AS
authors.lastname: Zweig
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.forename: W James
authors.initials: WJ
authors.lastname: Kent
mesh_terms: D001483:Base Sequence; D030561:Databases, Nucleic Acid; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D020407:Internet; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface