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
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Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature.
Nils Johan Fredriksson,Kerryn Elliott,Stefan Filges,Jimmy Van den Eynden,Anders Ståhlberg,Erik Larsson +5 more
TL;DR: It is shown that frequently recurring promoter mutations in melanoma occur almost exclusively at cytosines flanked by a distinct sequence signature, TTCCG, with TERT as a notable exception, with implications for the interpretation of somatic mutations in regulatory regions.
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Long non-coding RNAs in Colorectal Cancer: Progression and Future Directions.
TL;DR: This review focuses on recent findings on the involvement of lncRNAs in CRC oncogenesis and the lncRNA-based clinical implications in patients with CRC.
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Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage.
Yury A. Barbitoff,Dmitrii E. Polev,Andrey S. Glotov,Elena A. Serebryakova,Irina V. Shcherbakova,Artem M. Kiselev,Anna Kostareva,Oleg S. Glotov,Alexander V. Predeus +8 more
TL;DR: This study developed a set of statistical tools to systematically assess coverage of coding regions provided by several modern WES platforms, as well as PCR-free WGS, and identified main determinants of WES and WGS performance.
Journal ArticleDOI
The nuclear hypoxia-regulated NLUCAT1 long non-coding RNA contributes to an aggressive phenotype in lung adenocarcinoma through regulation of oxidative stress
Laura Moreno Leon,Marine Gautier,Richard Allan,Marius Ilie,Nicolas Nottet,Nicolas Pons,Agnès Paquet,Kevin Lebrigand,Marin Truchi,Julien Fassy,Virginie Magnone,Garrett Kinnebrew,Milan Radovich,Meyling Hua Chen Cheok,Pascal Barbry,Georges Vassaux,Charles-Hugo Marquette,Gilles Ponzio,Mircea Ivan,Nicolas Pottier,Paul Hofman,Bernard Mari,Roger Rezzonico +22 more
TL;DR: It is demonstrated that NLUCAT1 contributes to an aggressive phenotype in early-stage hypoxic tumors, suggesting it may represent a new potential therapeutic target in LUADs.
Journal ArticleDOI
Contribution of type W human endogenous retroviruses to the human genome : characterization of HERV-W proviral insertions and processed pseudogenes
TL;DR: The present work provides a detailed overview of the HERV-W contribution to the human genome and provides a robust genetic background useful to clarify HERv-W role in pathologies with poorly understood etiology, representing, to the authors' knowledge, the most complete and exhaustive HERVs-W dataset up to date.
References
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Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
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The Pfam protein families database
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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
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