ENCODE Data in the UCSC Genome Browser: Year 5 update

Kate R. Rosenbloom; Cricket A. Sloan; Venkat S. Malladi; Timothy R. Dreszer; Katrina Learned; Vanessa M. Kirkup; Matthew C. Wong; Morgan Maddren; Ruihua Fang; Steven G. Heitner; Brian T. Lee; Galt P. Barber; Rachel A. Harte; Mark Diekhans; Jeffrey C. Long; Steven P. Wilder; Ann S. Zweig; Donna Karolchik; Robert M. Kuhn; David Haussler; W. James Kent

doi:10.1093/nar/gks1172

ENCODE Data in the UCSC Genome Browser: Year 5 update

Kate R. Rosenbloom, Cricket A. Sloan, Venkat S. Malladi, Timothy R. Dreszer, Katrina Learned, Vanessa M. Kirkup, Matthew C. Wong, Morgan Maddren, Ruihua Fang, Steven G. Heitner, Brian T. Lee, Galt P. Barber, Rachel A. Harte, Mark Diekhans, Jeffrey C. Long, Steven P. Wilder, Ann S. Zweig, Donna Karolchik, Robert M. Kuhn, David HausslerW. James Kent

Research output: Contribution to journal › Article › peer-review

605 Scopus citations

Abstract

The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome, and its third year of investigations in the mouse genome. Since the last report in this journal, the ENCODE human data repertoire has grown by 898 new experiments (totaling 2886), accompanied by a major integrative analysis. In the mouse genome, results from 404 new experiments became available this year, increasing the total to 583, collected during the course of the project. The University of California, Santa Cruz, makes this data available on the public Genome Browser http://genome.ucsc.edu for visual browsing and data mining. Download of raw and processed data files are all supported. The ENCODE portal provides specialized tools and information about the ENCODE data sets.

Original language	English (US)
Pages (from-to)	D56-D63
Journal	Nucleic acids research
Volume	41
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gks1172
State	Published - Jan 1 2013
Externally published	Yes

ASJC Scopus subject areas

Genetics

Access to Document

10.1093/nar/gks1172

Cite this

Rosenbloom, K. R., Sloan, C. A., Malladi, V. S., Dreszer, T. R., Learned, K., Kirkup, V. M., Wong, M. C., Maddren, M., Fang, R., Heitner, S. G., Lee, B. T., Barber, G. P., Harte, R. A., Diekhans, M., Long, J. C., Wilder, S. P., Zweig, A. S., Karolchik, D., Kuhn, R. M., ... Kent, W. J. (2013). ENCODE Data in the UCSC Genome Browser: Year 5 update. Nucleic acids research, 41(D1), D56-D63. https://doi.org/10.1093/nar/gks1172

Rosenbloom, KR, Sloan, CA, Malladi, VS, Dreszer, TR, Learned, K, Kirkup, VM, Wong, MC, Maddren, M, Fang, R, Heitner, SG, Lee, BT, Barber, GP, Harte, RA, Diekhans, M, Long, JC, Wilder, SP, Zweig, AS, Karolchik, D, Kuhn, RM, Haussler, D & Kent, WJ 2013, 'ENCODE Data in the UCSC Genome Browser: Year 5 update', Nucleic acids research, vol. 41, no. D1, pp. D56-D63. https://doi.org/10.1093/nar/gks1172

@article{b32a06944aa041d2ab06086165b06f4c,

title = "ENCODE Data in the UCSC Genome Browser: Year 5 update",

abstract = "The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome, and its third year of investigations in the mouse genome. Since the last report in this journal, the ENCODE human data repertoire has grown by 898 new experiments (totaling 2886), accompanied by a major integrative analysis. In the mouse genome, results from 404 new experiments became available this year, increasing the total to 583, collected during the course of the project. The University of California, Santa Cruz, makes this data available on the public Genome Browser http://genome.ucsc.edu for visual browsing and data mining. Download of raw and processed data files are all supported. The ENCODE portal provides specialized tools and information about the ENCODE data sets.",

author = "Rosenbloom, {Kate R.} and Sloan, {Cricket A.} and Malladi, {Venkat S.} and Dreszer, {Timothy R.} and Katrina Learned and Kirkup, {Vanessa M.} and Wong, {Matthew C.} and Morgan Maddren and Ruihua Fang and Heitner, {Steven G.} and Lee, {Brian T.} and Barber, {Galt P.} and Harte, {Rachel A.} and Mark Diekhans and Long, {Jeffrey C.} and Wilder, {Steven P.} and Zweig, {Ann S.} and Donna Karolchik and Kuhn, {Robert M.} and David Haussler and Kent, {W. James}",

note = "Funding Information: National Human Genome Research Institute [5P41HG002371-12, 3P41HG002371-12S1 to the UCSC Center for Genomic Science; 5U41HG004568-04, 3U41HG004568-03S1 to the UCSC ENCODE Data Coordination Center]; Howard Hughes Medical Institute (to D.H.). Funding for open access charge: Howard Hughes Medical Institute.",

year = "2013",

month = jan,

day = "1",

doi = "10.1093/nar/gks1172",

language = "English (US)",

volume = "41",

pages = "D56--D63",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

TY - JOUR

T1 - ENCODE Data in the UCSC Genome Browser

T2 - Year 5 update

AU - Rosenbloom, Kate R.

AU - Sloan, Cricket A.

AU - Malladi, Venkat S.

AU - Dreszer, Timothy R.

AU - Learned, Katrina

AU - Kirkup, Vanessa M.

AU - Wong, Matthew C.

AU - Maddren, Morgan

AU - Fang, Ruihua

AU - Heitner, Steven G.

AU - Lee, Brian T.

AU - Barber, Galt P.

AU - Harte, Rachel A.

AU - Diekhans, Mark

AU - Long, Jeffrey C.

AU - Wilder, Steven P.

AU - Zweig, Ann S.

AU - Karolchik, Donna

AU - Kuhn, Robert M.

AU - Haussler, David

AU - Kent, W. James

N1 - Funding Information: National Human Genome Research Institute [5P41HG002371-12, 3P41HG002371-12S1 to the UCSC Center for Genomic Science; 5U41HG004568-04, 3U41HG004568-03S1 to the UCSC ENCODE Data Coordination Center]; Howard Hughes Medical Institute (to D.H.). Funding for open access charge: Howard Hughes Medical Institute.

PY - 2013/1/1

Y1 - 2013/1/1

N2 - The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome, and its third year of investigations in the mouse genome. Since the last report in this journal, the ENCODE human data repertoire has grown by 898 new experiments (totaling 2886), accompanied by a major integrative analysis. In the mouse genome, results from 404 new experiments became available this year, increasing the total to 583, collected during the course of the project. The University of California, Santa Cruz, makes this data available on the public Genome Browser http://genome.ucsc.edu for visual browsing and data mining. Download of raw and processed data files are all supported. The ENCODE portal provides specialized tools and information about the ENCODE data sets.

AB - The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome, and its third year of investigations in the mouse genome. Since the last report in this journal, the ENCODE human data repertoire has grown by 898 new experiments (totaling 2886), accompanied by a major integrative analysis. In the mouse genome, results from 404 new experiments became available this year, increasing the total to 583, collected during the course of the project. The University of California, Santa Cruz, makes this data available on the public Genome Browser http://genome.ucsc.edu for visual browsing and data mining. Download of raw and processed data files are all supported. The ENCODE portal provides specialized tools and information about the ENCODE data sets.

UR - http://www.scopus.com/inward/record.url?scp=84875945705&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84875945705&partnerID=8YFLogxK

U2 - 10.1093/nar/gks1172

DO - 10.1093/nar/gks1172

M3 - Article

C2 - 23193274

AN - SCOPUS:84875945705

SN - 0305-1048

VL - 41

SP - D56-D63

JO - Nucleic acids research

JF - Nucleic acids research

IS - D1

ER -

ENCODE Data in the UCSC Genome Browser: Year 5 update

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this