NONCODEV5: a comprehensive annotation database for long non-coding RNAs.
Shuangsang Fang,Lili Zhang,Jin-Cheng Guo,Jin-Cheng Guo,Yiwei Niu,Yang Wu,Hui Li,Lianhe Zhao,XiYuan Li,Xueyi Teng,Xianhui Sun,Liang Sun,Michael Q. Zhang,Runsheng Chen,Yi Zhao +14 more
TL;DR: The ncRNA data set was expanded by collecting newly identified ncRNAs from literature published over the past two years and integration of the latest versions of RefSeq and Ensembl.
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Abstract: NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). Since NONCODE 2016 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of next-generation sequencing, which has produced an explosion of newly identified data. The third-generation sequencing revolution has also offered longer and more accurate annotations. Moreover, accumulating evidence confirmed by biological experiments has provided more comprehensive knowledge of lncRNA functions. The ncRNA data set was expanded by collecting newly identified ncRNAs from literature published over the past two years and integration of the latest versions of RefSeq and Ensembl. Additionally, pig was included in the database for the first time, bringing the total number of species to 17. The number of lncRNAs in NONCODEv5 increased from 527 336 to 548 640. NONCODEv5 also introduced three important new features: (i) human lncRNA-disease relationships and single nucleotide polymorphism-lncRNA-disease relationships were constructed; (ii) human exosome lncRNA expression profiles were displayed; (iii) the RNA secondary structures of NONCODE human transcripts were predicted. NONCODEv5 is also accessible through http://www.noncode.org/.
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Citations
Gene regulation by long non-coding RNAs and its biological functions.
TL;DR: A review of the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications is presented in this article.
Long non-coding RNAs: definitions, functions, challenges and recommendations
John S. Mattick,Paulo P. Amaral,P. Carninci,Susan Carpenter,Howard Y. Chang,Ling-Ling Chen,Runsheng Chen,Caroline Dean,Marcel E. Dinger,Katherine A. Fitzgerald,Thomas R. Gingeras,Mitchell Guttman,Tetsuro Hirose,Maite Huarte,Rory Johnson,Chandrasekhar Kanduri,Philipp Kapranov,Jeanne B. Lawrence,Jeannie T. Lee,Joshua T. Mendell,Tim R. Mercer,Kathryn J. Moore,Shinichi Nakagawa,John L. Rinn,David L. Spector,Igor Ulitsky,Yue Wang,Jeremy E. Wilusz,Mian Hua Wu +28 more
TL;DR: The definition and nomenclature of long non-coding RNAs and their conservation, expression, phenotypic visibility, structure, and functions are discussed in this paper , where the authors also discuss research challenges and recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
Gencode 2021
Adam Frankish,Mark Diekhans,Irwin Jungreis,Julien Lagarde,Jane E. Loveland,Jonathan M. Mudge,Cristina Sisu,James C. Wright,Joel Armstrong,If Barnes,Andrew Berry,Alexandra Bignell,Carles Boix,S. Carbonell Sala,Fiona Cunningham,T. Di Domenico,Sarah Donaldson,Ian T. Fiddes,C. Garcia Giron,José M. González,Tiago Grego,Matthew Hardy,Thibaut Hourlier,Kerstin Howe,Toby Hunt,Osagie G. Izuogu,Rory Johnson,Fergal J. Martin,Laura Martinez,S. Mohanan,Paul R. Muir,Fabio C. P. Navarro,Anne Parker,Baikang Pei,Fernando Pozo,F. C. Riera,Magali Ruffier,Bianca M. Schmitt,E. Stapleton,Marie Marthe Suner,I. Sycheva,Barbara Uszczynska-Ratajczak,Maxim Y Wolf,Jinrui Xu,Y. T. Yang,Andrew D. Yates,Daniel R. Zerbino,Yan Zhang,Jyoti S. Choudhary,Mark Gerstein,Roderic Guigó,Tim Hubbard,Manolis Kellis,Benedict Paten,Michael L. Tress,Paul Flicek +55 more
TL;DR: The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics as mentioned in this paper. But the annotation process does not support the creation of transcript structures and the determination of their function.
Towards a complete map of the human long non-coding RNA transcriptome
TL;DR: The state of currently available long non-coding RNA annotations and the impact of emerging technologies such as long-read sequencing are discussed.
LNCipedia 5: towards a reference set of human long non-coding RNAs.
Pieter-Jan Volders,Jasper Anckaert,Kenneth Verheggen,Justine Nuytens,Lennart Martens,Pieter Mestdagh,Jo Vandesompele +6 more
TL;DR: The fifth release of the human lncRNA database LNCipedia is presented, with the most notable improvements include manual literature curation of 2482 lncRNAs articles and the use of official gene symbols when available.
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