lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
Xiu Cheng Quek,Daniel W. Thomson,Jesper L.V. Maag,Jesper L.V. Maag,Nenad Bartonicek,Bethany Signal,Michael B. Clark,Brian S. Gloss,Marcel E. Dinger,Marcel E. Dinger +9 more
TLDR
The lncRNAdb database as discussed by the authors provides users with a comprehensive, manually curated reference database of 287 eukaryotic long noncoding RNA (lncRNA) genes that have been described independently in the scientific literature.Abstract:
Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. In addition to capturing a great proportion of the recent literature describing functions for individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater accessibility to sequence information, expression data and the literature. The new features in lncRNAdb include the integration of Illumina Body Atlas expression profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct download or a REST API. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration.read more
Citations
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Journal ArticleDOI
Endogenous microRNA sponges: evidence and controversy.
TL;DR: The evidence for and against the ceRNA hypothesis are critically evaluated to assess the impact of endogenous miRNA-sponge interactions and to propose an alternative function for messenger RNAs.
Journal ArticleDOI
An atlas of human long non-coding RNAs with accurate 5′ ends
Chung-Chau Hon,Jordan A. Ramilowski,Jayson Harshbarger,Nicolas Bertin,Nicolas Bertin,Owen J. L. Rackham,Owen J. L. Rackham,Julian Gough,Elena Denisenko,Sebastian Schmeier,Thomas M. Poulsen,Jessica Severin,Marina Lizio,Hideya Kawaji,Takeya Kasukawa,Masayoshi Itoh,A. Maxwell Burroughs,Shohei Noma,Sarah Djebali,Sarah Djebali,Tanvir Alam,Yulia A. Medvedeva,Alison C. Testa,Leonard Lipovich,Chi Wai Yip,Imad Abugessaisa,Mickal Mendez,Akira Hasegawa,Dave Tang,Timo Lassmann,Peter Heutink,Magda Babina,Christine A. Wells,Christine A. Wells,Soichi Kojima,Yukio Nakamura,Harukazu Suzuki,Carsten O. Daub,Michiel J. L. de Hoon,Erik Arner,Yoshihide Hayashizaki,Piero Carninci,Alistair R. R. Forrest +42 more
TL;DR: This work integrates multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5′ ends and expression profiles across 1,829 samples from the major human primary cell types and tissues, identifying 19,175 potentially functional lncRNAs in the human genome.
Journal ArticleDOI
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features.
TL;DR: The coding potential calculator CPC1 is upgraded to CPC2, which runs ∼1000 times faster than CPC1 and exhibits superior accuracy compared with CPC1, especially for long non-coding transcripts.
Journal ArticleDOI
Colorectal Carcinoma: A General Overview and Future Perspectives in Colorectal Cancer
Inés Mármol,Cristina Sánchez-de-Diego,Alberto Pradilla Dieste,Elena Cerrada,María Jesús Rodriguez Yoldi +4 more
TL;DR: The choice of first-line treatment in CRC follows a multimodal approach based on tumour-related characteristics and usually comprises surgical resection followed by chemotherapy combined with monoclonal antibodies or proteins against vascular endothelial growth factor (VEGF) and epidermal growth receptor (EGFR).
Journal ArticleDOI
Non-coding RNA: what is functional and what is junk?
TL;DR: How to determine whether any given ncRNA has a function is discussed, and it is advocated that in the absence of any such data, the appropriate null hypothesis is that the RNA in question is junk.
References
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TL;DR: Evidence that three-quarters of the human genome is capable of being transcribed is reported, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs that prompt a redefinition of the concept of a gene.
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