GENCODE: The reference human genome annotation for The ENCODE Project
Jennifer Harrow,Adam Frankish,José M. González,Electra Tapanari,Mark Diekhans,Felix Kokocinski,Bronwen Aken,Daniel Barrell,Amonida Zadissa,Stephen M. J. Searle,If H. A. Barnes,Alexandra Bignell,Veronika Boychenko,Toby Hunt,M. Kay,Gaurab Mukherjee,Jeena Rajan,Gloria Despacio-Reyes,Gary Saunders,Charles A. Steward,Rachel A. Harte,Michael F. Lin,Cédric Howald,Andrea Tanzer,Thomas Derrien,Jacqueline Chrast,Nathalie Walters,Suganthi Balasubramanian,Baikang Pei,Michael L. Tress,Jose Manuel Rodriguez,Iakes Ezkurdia,Jeltje Van Baren,Michael R. Brent,David Haussler,Manolis Kellis,Alfonso Valencia,Alexandre Reymond,Mark Gerstein,Roderic Guigó,Tim Hubbard +40 more
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TLDR
This work has examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites, and over one-third of GENCODE protein-Coding genes aresupported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas.Abstract:
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.read more
Citations
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PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations
Mihir A Kamat,James A. Blackshaw,Robin Young,Praveen Surendran,Stephen Burgess,John Danesh,Adam S. Butterworth,James R Staley +7 more
TL;DR: A major update of PhenoScanner is presented, including over 150 million genetic variants and more than 65 billion associations with diseases and traits, gene expression, metabolite and protein levels, and epigenetic markers.
Journal ArticleDOI
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
Valerie A. Schneider,Tina A. Graves-Lindsay,Kerstin Howe,Nathan Bouk,Hsiu-Chuan Chen,Paul Kitts,Terence Murphy,Kim D. Pruitt,Françoise Thibaud-Nissen,Derek Albracht,Robert S. Fulton,Milinn Kremitzki,Vincent Magrini,Chris Markovic,Sean McGrath,Karyn Meltz Steinberg,Kate Auger,William Chow,Joanna Collins,Glenn Harden,Tim Hubbard,Sarah Pelan,Jared T. Simpson,Glen Threadgold,James Torrance,Jonathan Wood,Laura Clarke,Sergey Koren,Matthew Boitano,Paul Peluso,Heng Li,Chen-Shan Chin,Adam M. Phillippy,Richard Durbin,Richard K. Wilson,Paul Flicek,Evan E. Eichler,Deanna M. Church +37 more
TL;DR: It is asserted that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote the understanding of human biology and advance the efforts to improve health.
Journal ArticleDOI
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs.
TL;DR: It is observed with a large set of RNA-seq data covering a wide array of human tissue types that the majority of the genome is indeed transcribed, corroborating recent observations by the ENCODE project and finding that intergenic regions encode far more long intergenic noncoding RNAs (lincRNAs) than previously described, helping to resolve the discrepancy between the vast amount of observed intergenic transcription and the limited number of previously known linc RNAs.
Journal ArticleDOI
Correlation of circular RNA abundance with proliferation--exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues.
Anna Bachmayr-Heyda,Agnes T. Reiner,Katharina Auer,Nyamdelger Sukhbaatar,Stefanie Aust,Thomas Bachleitner-Hofmann,Ildiko Mesteri,Thomas W. Grunt,Robert Zeillinger,Dietmar Pils +9 more
TL;DR: The first to report a global reduction of circular RNA abundance in colorectal cancer cell lines and cancer compared to normal tissues is reported and a negative correlation of global circular RNAs abundance and proliferation is discovered.
Journal ArticleDOI
The UCSC Genome Browser database: 2016 update.
Matthew L. Speir,Ann S. Zweig,Kate R. Rosenbloom,Brian J. Raney,Benedict Paten,Parisa Nejad,Brian T. Lee,Katrina Learned,Donna Karolchik,Angie S. Hinrichs,Steve Heitner,Rachel A. Harte,Maximilian Haeussler,Luvina Guruvadoo,Pauline A. Fujita,Christopher Eisenhart,Mark Diekhans,Hiram Clawson,Jonathan Casper,Galt P. Barber,David Haussler,Robert M. Kuhn,W. James Kent +22 more
TL;DR: The UCSC Genome Browser has greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.
References
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