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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Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci.
Lam C. Tsoi,Sarah L. Spain,Sarah L. Spain,Eva Ellinghaus,Philip E. Stuart,Francesca Capon,Joanne Knight,Joanne Knight,Trilokraj Tejasvi,Hyun Min Kang,Michael H. Allen,Sylviane Lambert,Stefan W. Stoll,Stephan Weidinger,Johann E. Gudjonsson,Sulev Kõks,Külli Kingo,Tõnu Esko,Sayantan Das,Andres Metspalu,Michael Weichenthal,Charlotta Enerbäck,Gerald G. Krueger,John J. Voorhees,Vinod Chandran,Cheryl F. Rosen,Proton Rahman,Dafna D. Gladman,André Reis,Rajan P. Nair,Andre Franke,Jonathan Barker,Gonçalo R. Abecasis,Richard C. Trembath,James T. Elder,James T. Elder +35 more
TL;DR: The combined analysis, consisting of over 15,000 cases and 27,000 controls, identifies five new psoriasis susceptibility loci at genomewide significance, and demonstrates that NFKBIZ is a TRAF3IP2–dependent target of IL-17 signaling in human skin keratinocytes, thereby functionally linking two strong candidate genes.
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Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
Ana C. Marques,Jim R. Hughes,Bryony Graham,Monika S. Kowalczyk,Monika S. Kowalczyk,Doug Higgs,Chris P. Ponting +6 more
TL;DR: In this article, the sites of initiation of intergenic lncRNAs in mouse erythropoiesis were determined, allowing them to distinguish two similarly abundant classes of transcripts, 5′ capped and polyadenylated RNA transcripts.
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Choice of transcripts and software has a large effect on variant annotation
Davis J. McCarthy,Davis J. McCarthy,Peter Humburg,Alexander Kanapin,Manuel A. Rivas,Kyle J. Gaulton,Jean-Baptiste Cazier,Peter Donnelly,Peter Donnelly +8 more
TL;DR: The extent of differences in annotation of 80 million variants from a whole-genome sequencing study is quantified and the types of apparent errors made by Annovar and VEP are characterised and discussed to discuss their impact on the analysis of DNA variants in genome sequencing studies.
Journal ArticleDOI
Landscape of stimulation-responsive chromatin across diverse human immune cells.
Diego Calderon,Michelle L.T. Nguyen,Anja Mezger,Anja Mezger,Arwa Kathiria,Fabian Müller,Vinh Son Nguyen,Ninnia Lescano,Beijing Wu,John Trombetta,Jessica V. Ribado,David A. Knowles,Ziyue Gao,Ziyue Gao,Franziska Blaeschke,Franziska Blaeschke,Audrey Parent,Trevor D. Burt,Mark S. Anderson,Lindsey A. Criswell,William J. Greenleaf,Alexander Marson,Jonathan K. Pritchard,Jonathan K. Pritchard +23 more
TL;DR: Analysis of gene expression and open chromatin regions in up to 32 immune cell populations under resting and stimulated conditions identifies widespread chromatin remodeling and shared response elements between stimulated B and T cells.
Journal ArticleDOI
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation
Shaoke Lou,Heung Man Lee,Hao Qin,Jing-Woei Li,Zhibo Gao,Xin Liu,Landon L Chan,Vincent Kl Lam,Wing-Yee So,Ying Wang,Si Lok,Jun Wang,Ronald Cw Ma,Stephen Kwok-Wing Tsui,Juliana C.N. Chan,Ting-Fung Chan,Kevin Y. Yip +16 more
TL;DR: An integrated analysis of whole-genome bisulfite sequencing and RNA sequencing data from human samples and cell lines finds that while promoter methylation inversely correlates with gene expression as generally observed, the repressive effect is clear only on genes with a very high DNA methylation level.
References
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