ENCODE
From Wikipedia, the free encyclopedia
ENCODE (the ENCyclopedia Of DNA Elements) is a public research consortium launched by the US National Human Genome Research Institute (NHGRI) in September 2003. 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.
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[edit] 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 kf>genome.gov | ENCODE Project Target Selection Process and Target Regions</ref> 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. This data can be found here. The pilot phase was successfully finished and the result were published in June 2007 in Nature[1] and a special issue of Genome Research.[2]
[edit] Technology Phase
The concurrent phase to this is the technology development phase, which aims to investigate and develop new, high throughput techniques and protocols suitable for use in the ENCODE project.
[edit] Production Phase
The final phase of the ENCODE project has now been started. It aims to rigorously analyse the entire genome using the best methods and technologies identified in the first two phases. Funding has been granted to seven principal investigators from the U.S. and the U.K. (Bradley Bernstein, Gregory Crawford, Thomas Gingeras, Tim Hubbard, Richard Myers, Michael Snyder, John Stamatoyannopoulos).
[edit] 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.[3] 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.[3]
Funding for the modENCODE project was announced by the NIH in 2007 and included several different research institutions in the U.S.[4] [5]
[edit] See also
[edit] Notes
- ^ Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature (publication)
- ^ Special Issue with pilot phase results, Genome Research (publication)
- ^ a b "The modENCODE Project: Model Organism ENCyclopedia Of DNA Elements (modENCODE)". NHGRI website. http://www.genome.gov/26524507. Retrieved 2008-11-13.
- ^ "modENCODE Participants and Projects". NHGRI website. http://www.genome.gov/26524648. Retrieved 2008-11-13.
- ^ "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.
