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
Reads0
Chats0
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
More filters
Journal ArticleDOI
Drug Repurposing: The Anthelmintics Niclosamide and Nitazoxanide are Potent TMEM16A Antagonists that Fully Bronchodilate Airways
Kent Miner,Katja Labitzke,Benxian Liu,Paul Wang,Kathryn Henckels,Kevin Gaida,Robin Elliott,Jian J. Chen,Longbin Liu,Anh Leith,Esther S. Trueblood,Kelly Hensley,Xing-Zhong Xia,Oliver Homann,Brian D. Bennett,Mike Fiorino,John Whoriskey,Gang Yu,Sabine S. Escobar,Min Wong,Teresa L. Born,Alison L. Budelsky,M.R. Comeau,Dirk E. Smith,Jonathan E Phillips,James A. Johnston,Joe McGivern,Kerstin Weikl,David Powers,Karl Kunzelmann,Deanna Mohn,Andreas Hochheimer,John K. Sullivan +32 more
TL;DR: For the first time, antagonists of TMEM16A and repositioning of niclosamide and nitazoxanide represent an important additional treatment for patients with severe asthma and COPD that is poorly controlled with existing therapies.
Journal ArticleDOI
MicroRNA Profiling of Neurons Generated Using Induced Pluripotent Stem Cells Derived from Patients with Schizophrenia and Schizoaffective Disorder, and 22q11.2 Del
Dejian Zhao,Mingyan Lin,Jian Chen,Erika Pedrosa,Anastasia Hrabovsky,H. Matthew Fourcade,Deyou Zheng,Herbert M. Lachman +7 more
TL;DR: Differentially expressed miRNAs previously identified using autopsy samples and peripheral cells, both of which have significant methodological problems, are indeed disrupted in neuropsychiatric disorders and likely have an underlying genetic basis.
Journal ArticleDOI
APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism
Ting-Wen Chen,Chi-Ching Lee,Hsuan Liu,Chi Sheng Wu,Chi Sheng Wu,Curtis R. Pickering,Po-Jung Huang,Jing Wang,Ian Yi-Feng Chang,Yuan Ming Yeh,Chih De Chen,Hsin-Pai Li,Ji Dung Luo,Bertrand Chin-Ming Tan,Timothy En Haw Chan,Chuen Hsueh,Chuen Hsueh,Lichieh Julie Chu,Lichieh Julie Chu,Yi-Ting Chen,Bing Zhang,Chia Yu Yang,Chia Yu Yang,Chih-Ching Wu,Chih-Ching Wu,Chia-Wei Hsu,Lai-Chu See,Petrus Tang,Jau-Song Yu,Jau-Song Yu,Wei-Chao Liao,Wei-Chao Liao,Wei Fan Chiang,Henry Rodriguez,Jeffrey N. Myers,Kai-Ping Chang,Kai-Ping Chang,Yu-Sun Chang,Yu-Sun Chang +38 more
TL;DR: The authors show that OSCC in Taiwanese show a frequent deletion polymorphism in the cytidine deaminases gene cluster APOBEC3 resulting in increased expression of A3A, which is shown to be of clinical prognostic relevance.
Journal ArticleDOI
KDM5 histone demethylases repress immune response via suppression of STING
Lizhen Wu,Jian Cao,Wesley L. Cai,Sabine Lang,John R. Horton,Daniel J. Jansen,Zongzhi Liu,Jocelyn F. Chen,Meiling Zhang,Bryan T. Mott,Katherine Pohida,Ganesha Rai,Stephen C. Kales,Mark J. Henderson,Xin Hu,Ajit Jadhav,David J. Maloney,Anton Simeonov,Shu Zhu,Akiko Iwasaki,Akiko Iwasaki,Matthew D. Hall,Xiaodong Cheng,Gerald S. Shadel,Gerald S. Shadel,Qin Yan +25 more
TL;DR: A novel epigenetic regulatory pathway of immune response is demonstrated and it is suggested that KDM5 demethylases are potential targets for antipathogen treatment and anticancer immunotherapy.
Journal ArticleDOI
Integrative Transcriptome Analyses of Metabolic Responses in Mice Define Pivotal LncRNA Metabolic Regulators.
TL;DR: It is supported that a class of lncRNAs function as important metabolic regulators and establishes a framework for systemically investigating the role of lNCRNAs in physiological homeostasis.
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.
Related Papers (5)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more