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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A large electronic-health-record-based genome-wide study of serum lipids.
Thomas J. Hoffmann,Elizabeth Theusch,Tanushree Haldar,Dilrini K. Ranatunga,Eric Jorgenson,Marisa W. Medina,Mark N. Kvale,Pui-Yan Kwok,Catherine Schaefer,Ronald M. Krauss,Carlos Iribarren,Neil Risch,Neil Risch +12 more
TL;DR: Using EHR pharmacy data, both LDL and triglyceride genetic risk scores were strongly predictive of age at initiation of lipid-lowering treatment and highlight the value of longitudinal EHRs for identifying new genetic features of cholesterol and lipoprotein metabolism with implications for lipid treatment and risk of coronary heart disease.
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The genetic basis and cell of origin of mixed phenotype acute leukaemia
Thomas B. Alexander,Thomas B. Alexander,Zhaohui Gu,Ilaria Iacobucci,Kirsten Dickerson,John K. Choi,Beisi Xu,Debbie Payne-Turner,Hiroki Yoshihara,Mignon L. Loh,John T. Horan,Barbara Buldini,Giuseppe Basso,Sarah Elitzur,Valerie de Haas,C. Michel Zwaan,Allen Eng Juh Yeoh,Dirk Reinhardt,Daisuke Tomizawa,Nobutaka Kiyokawa,Tim Lammens,Barbara De Moerloose,Daniel Catchpoole,Hiroki Hori,Anthony V. Moorman,Andrew S. Moore,Ondrej Hrusak,Soheil Meshinchi,Soheil Meshinchi,Etan Orgel,Meenakshi Devidas,Michael J. Borowitz,Brent L. Wood,Nyla A. Heerema,Andrew Carrol,Yung-Li Yang,Malcolm A. Smith,Tanja M. Davidsen,Leandro C. Hermida,Patee Gesuwan,Marco A. Marra,Yussanne Ma,Andrew J. Mungall,Richard A. Moore,Steven J.M. Jones,Marcus B. Valentine,Laura J. Janke,Jeffrey E. Rubnitz,Ching-Hon Pui,Liang Ding,Yu Liu,Jinghui Zhang,Kim E. Nichols,James R. Downing,Xueyuan Cao,Lei Shi,Stanley Pounds,Scott Newman,Deqing Pei,Jaime M. Guidry Auvil,Daniela S. Gerhard,Stephen P. Hunger,Hiroto Inaba,Charles G. Mullighan +63 more
TL;DR: A large-scale genomics study shows that the cell of origin and founding mutations determine disease subtype and lead to the expression of multiple haematopoietic lineage-defining antigens in mixed phenotype acute leukaemia.
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Long Noncoding RNA PVT1 Promotes Non-Small Cell Lung Cancer Cell Proliferation through Epigenetically Regulating LATS2 Expression.
Li Wan,Ming Sun,Guo-Jian Liu,Chenchen Wei,Erbao Zhang,Rong Kong,Tongpeng Xu,Ming-de Huang,Zhaoxia Wang +8 more
TL;DR: Functional analysis revealed that knockdown of PVT1 inhibited NSCLC cell proliferation and induced apoptosis both in vitro and in vivo, and indicated that PVT 1/EZH2/LATS2 interactions might serve as new target for lung adenocarcinoma diagnosis and therapy.
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Finding the active genes in deep RNA-seq gene expression studies.
TL;DR: The zFPKM normalization method accurately separates the biologically relevant genes in a cell from the ultralow-expression noisy genes that have repressed promoters, providing important guidance for the design of RNA-seq studies of gene expression.
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Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins
Alfonso Buil,Andrew A. Brown,Tuuli Lappalainen,Ana Viñuela,Matthew N. Davies,Hou-Feng Zheng,J. Brent Richards,Daniel Glass,Kerrin S. Small,Richard Durbin,Tim D. Spector,Emmanouil T. Dermitzakis +11 more
TL;DR: A model where ASE requires genetic variability in cis, a difference in the sequence of both alleles, but where the magnitude of the ASE effect depends on trans genetic and environmental factors that interact with the cis genetic variants is proposed.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
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