Open AccessJournal Article
An integrated encyclopedia of DNA elements in the human genome.
TLDR
The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.Abstract:
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.read more
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The Genotype-Tissue Expression (GTEx) project
John T. Lonsdale,Jeffrey Thomas,Mike Salvatore,Rebecca Phillips,Edmund Lo,Saboor Shad,Richard Hasz,Gary Walters,Fernando U. Garcia,Nancy Young,Barbara A. Foster,Mike Moser,Ellen Karasik,Bryan Gillard,Kimberley Ramsey,Susan L. Sullivan,Jason Bridge,Harold Magazine,John Syron,Johnelle Fleming,Laura A. Siminoff,Heather M. Traino,Maghboeba Mosavel,Laura Barker,Scott D. Jewell,Daniel C. Rohrer,Dan Maxim,Dana Filkins,Philip Harbach,Eddie Cortadillo,Bree Berghuis,Lisa Turner,Eric Hudson,Kristin Feenstra,Leslie H. Sobin,James A. Robb,Phillip Branton,Greg E. Korzeniewski,Charles Shive,David Tabor,Liqun Qi,Kevin Groch,Sreenath Nampally,Steve Buia,Angela Zimmerman,Anna M. Smith,Robin Burges,Karna Robinson,Kim Valentino,Deborah Bradbury,Mark Cosentino,Norma Diaz-Mayoral,Mary Kennedy,Theresa Engel,Penelope Williams,Kenyon Erickson,Kristin G. Ardlie,Wendy Winckler,Gad Getz,Gad Getz,David S. DeLuca,MacArthur Daniel MacArthur,MacArthur Daniel MacArthur,Manolis Kellis,Alexander Thomson,Taylor Young,Ellen Gelfand,Molly Donovan,Yan Meng,George B. Grant,Deborah C. Mash,Yvonne Marcus,Margaret J. Basile,Jun Liu,Jun Zhu,Zhidong Tu,Nancy J. Cox,Dan L. Nicolae,Eric R. Gamazon,Hae Kyung Im,Anuar Konkashbaev,Jonathan K. Pritchard,Jonathan K. Pritchard,Matthew Stevens,Timothée Flutre,Xiaoquan Wen,Emmanouil T. Dermitzakis,Tuuli Lappalainen,Roderic Guigó,Jean Monlong,Michael Sammeth,Daphne Koller,Alexis Battle,Sara Mostafavi,Mark I. McCarthy,Manual Rivas,Julian Maller,Ivan Rusyn,Andrew B. Nobel,Fred A. Wright,Andrey A. Shabalin,Mike Feolo,Nataliya Sharopova,Anne Sturcke,Justin Paschal,James M. Anderson,Elizabeth L. Wilder,Leslie Derr,Eric D. Green,Jeffery P. Struewing,Gary F. Temple,Simona Volpi,Joy T. Boyer,Elizabeth J. Thomson,Mark S. Guyer,Cathy Ng,Assya Abdallah,Deborah Colantuoni,Thomas R. Insel,Susan E. Koester,Roger Little,Patrick Bender,Thomas Lehner,Yin Yao,Carolyn C. Compton,Jimmie B. Vaught,Sherilyn Sawyer,Nicole C. Lockhart,Joanne P. Demchok,Helen F. Moore +129 more
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A general framework for estimating the relative pathogenicity of human genetic variants
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TL;DR: Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
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Landscape of transcription in human cells
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TL;DR: Evidence that three-quarters of the human genome is capable of being transcribed is reported, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs that prompt a redefinition of the concept of a gene.
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