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
Long Noncoding RNA in Cancer: Wiring Signaling Circuitry
Chunru Lin,Liuqing Yang +1 more
TL;DR: The mechanisms by which lncRNAs regulate cellular responses to extracellular signals are reviewed and their clinical potential as diagnostic indicators, stratification markers, and therapeutic targets of combinatorial treatments are discussed.
Journal ArticleDOI
Long noncoding RNAs are rarely translated in two human cell lines
Balazs Banfai,Hui Jia,Jainab Khatun,Emily J. Wood,Brian A. Risk,William E. Gundling,Anshul Kundaje,Harsha P. Gunawardena,Yanbao Yu,Ling Xie,Krzysztof Krajewski,Brian D. Strahl,Xian Chen,Peter J. Bickel,Morgan C. Giddings,James B. Brown,Leonard Lipovich +16 more
TL;DR: It is concluded that with very few exceptions, ribosomes are able to distinguish coding from noncoding transcripts and, hence, that ectopic translation and cryptic mRNAs are rare in the human lncRNAome.
Journal ArticleDOI
Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia
Thomas Trimarchi,Thomas Trimarchi,Erhan Bilal,Panagiotis Ntziachristos,Panagiotis Ntziachristos,Giulia Fabbri,Riccardo Dalla-Favera,Aristotelis Tsirigos,Iannis Aifantis,Iannis Aifantis +9 more
TL;DR: It is shown that one specific Notch-regulated lncRNA, LUNAR1, is required for efficient T-ALL growth in vitro and in vivo due to its ability to enhance IGF1R mRNA expression and sustain IGF1 signaling.
Journal ArticleDOI
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
TL;DR: This Review discusses bioinformatics tools that have been devised to handle the numerous characteristic features of these long-range data types, with applications in genome assembly, genetic variant detection, haplotype phasing, transcriptomics and epigenomics.
Journal ArticleDOI
Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes
Anita Sveen,Anita Sveen,Sami Kilpinen,A Ruusulehto,Ragnhild A. Lothe,Ragnhild A. Lothe,Rolf Inge Skotheim,Rolf Inge Skotheim +7 more
TL;DR: This review provides an overview of aberrant RNA splicing and its regulation in cancer, and proposes 24 novel cancer-critical splicing factors predicted from somatic mutations.
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