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The ENCODE Project at UC Santa Cruz

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 dataset...

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Autores principales: Thomas, Daryl J., Rosenbloom, Kate R., Clawson, Hiram, Hinrichs, Angie S., Trumbower, Heather, Raney, Brian J., Karolchik, Donna, Barber, Galt P., Harte, Rachel A., Hillman-Jackson, Jennifer, Kuhn, Robert M., Rhead, Brooke L., Smith, Kayla E., Thakkapallayil, Archana, Zweig, Ann S., Haussler, David, Kent, W. James
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781110/
https://www.ncbi.nlm.nih.gov/pubmed/17166863
http://dx.doi.org/10.1093/nar/gkl1017
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author Thomas, Daryl J.
Rosenbloom, Kate R.
Clawson, Hiram
Hinrichs, Angie S.
Trumbower, Heather
Raney, Brian J.
Karolchik, Donna
Barber, Galt P.
Harte, Rachel A.
Hillman-Jackson, Jennifer
Kuhn, Robert M.
Rhead, Brooke L.
Smith, Kayla E.
Thakkapallayil, Archana
Zweig, Ann S.
Haussler, David
Kent, W. James
author_facet Thomas, Daryl J.
Rosenbloom, Kate R.
Clawson, Hiram
Hinrichs, Angie S.
Trumbower, Heather
Raney, Brian J.
Karolchik, Donna
Barber, Galt P.
Harte, Rachel A.
Hillman-Jackson, Jennifer
Kuhn, Robert M.
Rhead, Brooke L.
Smith, Kayla E.
Thakkapallayil, Archana
Zweig, Ann S.
Haussler, David
Kent, W. James
author_sort Thomas, Daryl J.
collection PubMed
description 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 () 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.
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spelling pubmed-17811102007-02-22 The ENCODE Project at UC Santa Cruz Thomas, Daryl J. Rosenbloom, Kate R. Clawson, Hiram Hinrichs, Angie S. Trumbower, Heather Raney, Brian J. Karolchik, Donna Barber, Galt P. Harte, Rachel A. Hillman-Jackson, Jennifer Kuhn, Robert M. Rhead, Brooke L. Smith, Kayla E. Thakkapallayil, Archana Zweig, Ann S. Haussler, David Kent, W. James Nucleic Acids Res Articles 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 () 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. Oxford University Press 2007-01 2006-12-13 /pmc/articles/PMC1781110/ /pubmed/17166863 http://dx.doi.org/10.1093/nar/gkl1017 Text en © 2006 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Thomas, Daryl J.
Rosenbloom, Kate R.
Clawson, Hiram
Hinrichs, Angie S.
Trumbower, Heather
Raney, Brian J.
Karolchik, Donna
Barber, Galt P.
Harte, Rachel A.
Hillman-Jackson, Jennifer
Kuhn, Robert M.
Rhead, Brooke L.
Smith, Kayla E.
Thakkapallayil, Archana
Zweig, Ann S.
Haussler, David
Kent, W. James
The ENCODE Project at UC Santa Cruz
title The ENCODE Project at UC Santa Cruz
title_full The ENCODE Project at UC Santa Cruz
title_fullStr The ENCODE Project at UC Santa Cruz
title_full_unstemmed The ENCODE Project at UC Santa Cruz
title_short The ENCODE Project at UC Santa Cruz
title_sort encode project at uc santa cruz
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781110/
https://www.ncbi.nlm.nih.gov/pubmed/17166863
http://dx.doi.org/10.1093/nar/gkl1017
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