ENCODE

ENCODE
ENCODE
Database.png
Content
Description whole-genome data
Contact
Research center University of California Santa Cruz
Laboratory Center for Biomolecular Science and Engineering
Authors Brian J Raney
Primary Citation Raney & al. (2011)[1]
Release date 2010
Access
Website http://encodeproject.org
Tools
Miscellaneous

ENCODE (the ENCyclopedia Of DNA Elements) is a public research consortium launched by the US National Human Genome Research Institute (NHGRI) in September 2003[2][3][4]. The goal is to find all functional elements in the human genome, one of the most critical projects by NHGRI after it completed the successful Human Genome Project. All data generated in the course of the project will be released rapidly into public databases.

Contents

Pilot phase

The project was initiated with a $12 million pilot phase. The aim of this was to evaluate a variety of different methods for use in later stages. Essentially this involved using a number of existing techniques to analyse a portion of the genome equal to about 1% (30mb). The results of these analyses will then be evaluated based on their ability to identify regions of DNA which are known or suspected to contain functional elements. 50% of the sample area selected for study under this phase was manually selected whilst the other 50% was selected at random.[5] The manually selected regions have been selected based on the presence of well studied genes and the availability of comparative data. Methods currently being evaluated include chromatin immunoprecipitation (ChIP) and quantitative PCR.

The ENCODE pilot project rapidly released all of its data into public databases.[6] The pilot phase was successfully finished and the results were published in June 2007 in Nature[3] and a special issue of Genome Research.[7]

Production Phase

Image of ENCODE data in the UCSC Genome Browser. This shows several tracks containing information on gene regulation. The gene on the left is transcribed in a wide variety of cells. The gene on the right is only transcribed in a few types of cells, including embryonic stem cells.

In September 2007 NHGRI began funding the production phase of the ENCODE project. In this phase, the goal is to analyze the entire genome and to conduct "additional pilot-scale studies."[8]


Like the pilot project, the production effort is organized as an open consortium. In October 2007, NHGRI awarded grants totaling more than $80 million over four years.[9] The production phase also includes a Data Coordination Center, a Data Analysis Center, and a Technology Development Effort.[10]

As of 2010 over 1000 genome-wide data sets have been produced by the ENCODE project. These data sets between them show what regions are transcribed into RNA, what regions are likely to control what genes are used in a particular type of cell, and what regions are associated with a wide variety of proteins. The primary assays used in ENCODE are ChIP-seq, DNAse Hypersensitivity, and RNA-seq, and assays of DNA methylation.

modENCODE project

The Model Organism ENCyclopedia Of DNA Elements (modENCODE) project is a continuation of the original ENCODE project targeting the identification of functional elements in selected model organism genomes, specifically, Drosophila melanogaster and Caenorhabditis elegans.[11] The extension to model organisms permits biological validation of the computational and experimental findings of the ENCODE project, something that is difficult or impossible to do in humans.[11]

Funding for the modENCODE project was announced by the NIH in 2007 and included several different research institutions in the US.[12][13]

In late 2010, the modENCODE consortium unveiled its first set of results with publications on annotation and integrative analysis of the worm and fly genomes in Science.[14][15] Data from these publications is available from modencode.org.

FactorBook

An analysis of transcription factor binding data generated by the ENCODE project is available in a web accessible repository factorbook.org.

See also

References

  1. ^ Raney, Brian J; Cline Melissa S, Rosenbloom Kate R, Dreszer Timothy R, Learned Katrina, Barber Galt P, Meyer Laurence R, Sloan Cricket A, Malladi Venkat S, Roskin Krishna M, Suh Bernard B, Hinrichs Angie S, Clawson Hiram, Zweig Ann S, Kirkup Vanessa, Fujita Pauline A, Rhead Brooke, Smith Kayla E, Pohl Andy, Kuhn Robert M, Karolchik Donna, Haussler David, Kent W James (Jan 2011). "ENCODE whole-genome data in the UCSC genome browser (2011 update)" (in eng). Nucleic Acids Res. (England) 39 (Database issue): D871-5. doi:10.1093/nar/gkq1017. PMC 3013645. PMID 21037257. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3013645. 
  2. ^ Becker, Peter B., ed (2011). "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)". PLoS Biology 9 (4): e1001046. doi:10.1371/journal.pbio.1001046. PMC 3079585. PMID 21526222. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3079585.  edit
  3. ^ a b Birney, E.; Stamatoyannopoulos, J. A.; Dutta, A.; Guigó, R.; Gingeras, T. R.; Margulies, E. H.; Weng, Z.; Snyder, M. et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447 (7146): 799–816. Bibcode 2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2212820.  edit
  4. ^ Guigó, R.; Flicek, P.; Abril, J. F.; Reymond, A.; Lagarde, J.; Denoeud, F.; Antonarakis, S.; Ashburner, M. et al. (2006). "EGASP: The human ENCODE Genome Annotation Assessment Project". Genome Biology 7: S2. doi:10.1186/gb-2006-7-s1-s2. PMC 1810551. PMID 16925836. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1810551.  edit
  5. ^ "ENCODE Pilot Project: Target Selection". The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01. http://www.genome.gov/10506161. Retrieved 2011-08-05. 
  6. ^ "ENCODE Project at UCSC". University of California at Santa Cruz. http://genome.ucsc.edu/ENCODE/. Retrieved 2011-08-05. 
  7. ^ Weinstock, G. M. (2007). "ENCODE: More genomic empowerment". Genome Research 17 (6): 667–668. doi:10.1101/gr.6534207. PMID 17567987.  edit
  8. ^ "Genome.gov | ENCODE and modENCODE Projects". The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01. http://www.genome.gov/10005107. Retrieved 2011-08-05. 
  9. ^ "National Human Genome Research Institute - Organization - The NIH Almanac - (NIH)". United States National Institutes of Health. http://www.nih.gov/about/almanac/organization/NHGRI.htm. Retrieved 2011-08-05. 
  10. ^ "Genome.gov | ENCODE Participants and Projects". The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01. http://www.genome.gov/26525220. Retrieved 2011-08-05. 
  11. ^ a b "The modENCODE Project: Model Organism ENCyclopedia Of DNA Elements (modENCODE)". NHGRI website. http://www.genome.gov/26524507. Retrieved 2008-11-13. 
  12. ^ "modENCODE Participants and Projects". NHGRI website. http://www.genome.gov/26524648. Retrieved 2008-11-13. 
  13. ^ "Berkeley Lab Life Sciences Awarded NIH Grants for Fruit Fly, Nematode Studies". Lawrence Berkeley National Laboratory website. 2007-05-14. http://www.lbl.gov/Science-Articles/Archive/LSD-modENCODE.html. Retrieved 2008-11-13. 
  14. ^ Gerstein, M. B.; Lu, Z. J.; Van Nostrand, E. L.; Cheng, C.; Arshinoff, B. I.; Liu, T.; Yip, K. Y.; Robilotto, R. et al. (2010). "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project". Science 330 (6012): 1775–1787. Bibcode 2010Sci...330.1775G. doi:10.1126/science.1196914. PMID 21177976.  edit
  15. ^ Roy, S.; Ernst, J.; Kharchenko, P. V.; Kheradpour, P.; Negre, N.; Eaton, M. L.; Landolin, J. M.; Bristow, C. A. et al. (2010). "Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE". Science 330 (6012): 1787–1797. Bibcode 2010Sci...330.1787R. doi:10.1126/science.1198374. PMID 21177974.  edit

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  • Encode — (с англ.  «зашифровывать, кодировать»): Связано с понятием «код» или «кодирование» Encode ApS  датская компания Encode SA  греческая компания ENCODE  Энциклопедия элементов ДНК См. также Character encoding  набор символов …   Википедия

  • Encode — may refer to: * Can be related to Code * Encode ApS, a Danish software company * ENCODE, the ENCyclopedia Of DNA Elementsee also* Encoding …   Wikipedia

  • encode — UK US /ɪnˈkəʊd/ US  / ˈkoʊd/ verb [T] ► IT to put information into a form in which it can be stored, and which can only be read using special technology or knowledge: »HTML is the programming language used to encode documents to that they can be… …   Financial and business terms

  • Encode —   [engl.], das Kodieren von Daten mit einem Encoder, auch das Verschlüsseln (Datenverschlüsselung) von Daten …   Universal-Lexikon

  • encode — 1919, from EN (Cf. en ) (1) make, put in + CODE (Cf. code). Computing sense is from 1955, usually shortened colloquially to code. Related: Encoded; encoding …   Etymology dictionary

  • encode — [v] encrypt cipher, conceal, cryptograph, make secret, put into code; concept 188 …   New thesaurus

  • encode — ► VERB ▪ convert into a coded form. DERIVATIVES encoder noun …   English terms dictionary

  • encode — [en kōd′, inkōd′] vt. encoded, encoding 1. to convert (a message, information, etc.) into code 2. to convert (data) by applying an electronic code encoder n …   English World dictionary

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