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
A GC-rich sequence feature in the 3' UTR directs UPF1-dependent mRNA decay in mammalian cells.
TL;DR: It is found that 3' U TR but not 5' UTRs or open reading frames of UPF1 targets have GC-rich motifs embedded in high GC-content regions, which highlight the important features of UpF1 target 3'UTRs.
Journal ArticleDOI
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation
Anurag Sethi,Mengting Gu,Emrah Gumusgoz,Landon L Chan,Koon-Kiu Yan,Joel Rozowsky,Iros Barozzi,Veena Afzal,Jennifer A. Akiyama,Ingrid Plajzer-Frick,Chengfei Yan,Catherine S. Novak,Momoe Kato,Tyler H. Garvin,Quan Pham,Anne N. Harrington,Brandon J. Mannion,Elizabeth Lee,Yoko Fukuda-Yuzawa,Axel Visel,Diane E. Dickel,Kevin Y. Yip,Richard E. Sutton,Len A. Pennacchio,Mark Gerstein +24 more
TL;DR: A framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features that can be transferred to predict mouse and human enhancers and examined the transcription factor binding patterns at predicted enhancers versus promoters.
Journal ArticleDOI
Functional transcriptomics in the post-ENCODE era
TL;DR: The current state of human transcriptome annotation is discussed, drawing on the experience gained in generating the GENCODE gene annotation set, and it is proposed that an understanding of the true overlap between transcriptional complexity and functionality will not be gained in the short term.
Journal ArticleDOI
MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer.
Arcadi Cipponi,Arcadi Cipponi,David L Goode,David L Goode,Justin Bedo,Justin Bedo,Justin Bedo,Mark J. McCabe,Mark J. McCabe,Marina Pajic,Marina Pajic,David R. Croucher,David R. Croucher,Alvaro Gonzalez Rajal,Simon Junankar,Simon Junankar,Darren N. Saunders,Pavel Lobachevsky,Anthony T. Papenfuss,Danielle Nessem,Max Nobis,Max Nobis,Sean C. Warren,Sean C. Warren,Paul Timpson,Paul Timpson,Mark J. Cowley,Mark J. Cowley,Ana Cristina Vargas,Min Ru Qiu,Min Ru Qiu,Daniele Generali,Shivakumar Keerthikumar,Shivakumar Keerthikumar,Uyen Nguyen,Niall M. Corcoran,Niall M. Corcoran,Georgina V. Long,Jean-Yves Blay,David Thomas,David Thomas +40 more
TL;DR: Sim is described in multiple in vitro and in vivo models of human cancers under nongenotoxic drug selection, paradoxically enhancing adaptation at a competing intrinsic fitness cost, and suggests synthetic lethal strategies to minimize resistance to anticancer therapy.
Journal ArticleDOI
Whole-Genome Alignment and Comparative Annotation.
TL;DR: The state of the genome alignment and comparative annotation fields and potential future directions for these fields in a new, large-scale era of comparative genomics are surveyed.
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