We propose establishing the UCSC ENCODE Data Coordination Center to collect, organize, store, and provide access to data from the ENCODE project and other related projects, based on the well-established UCSC Genome Browser. The UCSC browser is a robust, flexible platform that integrates a variety of features that make accessing genomic data both convenient and information-rich. As such, it has attained a high level of acceptance throughout the biology, bioinformatics, and biomedical research communities. During the pilot phase of the ENCODE project, involving 1% of the genome, UCSC has been the repository of sequence-based data. Through participation in the pilot phase, we have established cost-effective, high-throughput approaches for incorporating and displaying ENCODE data, and we have developed an effective interface to the consortium for uploading data files and methods documentation to our FTP site. Through ongoing expansion and improvement of our ENCODE browser, we have laid the groundwork for data management in the whole-genome phase of the project. UCSC's specific aims for participation as the ENCODE DCC are as follows: 1) coordinate closely with the ENCODE data providers to collect, store, and manage ENCODE sequence-based functional element data and related metadata;2) provide and maintain a long-term storage system for data from the ENCODE Consortium and related genomic projects;3) provide the ENCODE and public research communities with freely-available mechanisms to access, search, and analyze the ENCODE data;4) employ good software engineering practices to ensure that the ENCODE data are of the highest possible quality;and 5) foster collaboration with the biomedical community. Fundamental to understanding human biology and disease is the ability to identify and locate the functional elements in the human genome sequence. Both the effective presentation of experimental data and the ability to analyze sequence data using computational methods will help elucidate genomic function. Because the UCSC Genome Browser serves both of these purposes, it offers the ideal platform for ENCODE data.
| Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S et al. (2015) Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics 31:764-6 |
| Miga, Karen H; Eisenhart, Christopher; Kent, W James (2015) Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments. Nucleic Acids Res 43:e133 |
| Nguyen, Ngan; Hickey, Glenn; Zerbino, Daniel R et al. (2015) Building a pan-genome reference for a population. J Comput Biol 22:387-401 |
| Miga, Karen H; Newton, Yulia; Jain, Miten et al. (2014) Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res 24:697-707 |
| Raney, Brian J; Dreszer, Timothy R; Barber, Galt P et al. (2014) Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30:1003-5 |
| Rosenbloom, Kate R; Sloan, Cricket A; Malladi, Venkat S et al. (2013) ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res 41:D56-63 |
| Kuhn, Robert M; Haussler, David; Kent, W James (2013) The UCSC genome browser and associated tools. Brief Bioinform 14:144-61 |
| Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S et al. (2013) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 41:D64-9 |
| 1000 Genomes Project Consortium; Abecasis, Goncalo R; Auton, Adam et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491:56-65 |
| ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74 |
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