EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

Abstract Long non-coding RNAs (lncRNAs) play important functional roles in many diverse biological processes. However, not all expressed lncRNAs are functional. Thus, it is necessary to manually collect all experimentally validated functional lncRNAs (EVlncRNA) with their sequences, structures, and functions annotated in a central database. The first release of such a database (EVLncRNAs) was made using the literature prior to 1 May 2016. Since then (till 15 May 2020), 19 245 articles related to lncRNAs have been published. In EVLncRNAs 2.0, these articles were manually examined for a major expansion of the data collected. Specifically, the number of annotated EVlncRNAs, associated diseases, lncRNA-disease associations, and interaction records were increased by 260%, 320%, 484% and 537%, respectively. Moreover, the database has added several new categories: 8 lncRNA structures, 33 exosomal lncRNAs, 188 circular RNAs, and 1079 drug-resistant, chemoresistant, and stress-resistant lncRNAs. All records have checked against known retraction and fake articles. This release also comes with a highly interactive visual interaction network that facilitates users to track the underlying relations among lncRNAs, miRNAs, proteins, genes and other functional elements. Furthermore, it provides links to four new bioinformatics tools with improved data browsing and searching functionality. EVLncRNAs 2.0 is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs2/.

[1]  Yaoqi Zhou,et al.  Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network , 2020, Bioinform..

[2]  Anthony J. Cesnik,et al.  HyPR-MS for Multiplexed Discovery of MALAT1, NEAT1, and NORAD lncRNA Protein Interactomes. , 2018, Journal of proteome research.

[3]  Zhengrong Yin,et al.  The roles of exosomal miRNAs and lncRNAs in lung diseases. , 2019, Signal Transduction and Targeted Therapy.

[4]  Hui Xiao,et al.  NONCODE v3.0: integrative annotation of long noncoding RNAs , 2011, Nucleic Acids Res..

[5]  Marcel Schilling,et al.  Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. , 2014, Molecular cell.

[6]  W. Chng,et al.  EZH2 abnormalities in lymphoid malignancies: underlying mechanisms and therapeutic implications , 2019, Journal of Hematology & Oncology.

[7]  Shunmin He,et al.  NPInter v4.0: an integrated database of ncRNA interactions , 2019, Nucleic Acids Res..

[8]  Jeannie T. Lee,et al.  Long Noncoding RNAs: Past, Present, and Future , 2013, Genetics.

[9]  J. Wilusz.  Post-Transcriptional Gene Regulation , 2008, Methods In Molecular Biology™.

[10]  Howard Y. Chang,et al.  Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. , 2011, Molecular cell.

[11]  J. Michael Cherry,et al.  The Encyclopedia of DNA elements (ENCODE): data portal update , 2017, Nucleic Acids Res..

[12]  Qinghua Guo,et al.  LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse , 2018, Nucleic Acids Res..

[13]  Wei Wu,et al.  NONCODEv4: exploring the world of long non-coding RNA genes , 2013, Nucleic Acids Res..

[14]  J. Mendell,et al.  Functional Classification and Experimental Dissection of Long Noncoding RNAs , 2018, Cell.

[15]  Michael Q. Zhang,et al.  NONCODEV5: a comprehensive annotation database for long non-coding RNAs , 2017, Nucleic Acids Res..

[16]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[17]  John S. Mattick,et al.  lncRNAdb: a reference database for long noncoding RNAs , 2010, Nucleic Acids Res..

[18]  Thomas L. Madden,et al.  Database resources of the National Center for Biotechnology Information. , 2019, Nucleic acids research.

[19]  Li Wang,et al.  Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers , 2018, Nucleic Acids Res..

[20]  Yaoqi Zhou,et al.  RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning , 2019, Nature Communications.

[21]  Ruth L. Seal,et al.  Guidelines for human gene nomenclature , 2020, Nature Genetics.

[22]  Yi Zhao,et al.  NONCODE: an integrated knowledge database of non-coding RNAs , 2004, Nucleic Acids Res..

[23]  M. D. Simon,et al.  Capture hybridization analysis of RNA targets (CHART). , 2013, Current protocols in molecular biology.

[24]  D. Tollervey,et al.  Identification of miRNA-Target RNA Interactions Using CLASH. , 2016, Methods in molecular biology.

[25]  Gene W. Yeo,et al.  A large-scale binding and functional map of human RNA-binding proteins , 2020, Nature.

[26]  Michal Ziv-Ukelson,et al.  Rich Parameterization Improves RNA Structure Prediction , 2011, RECOMB.

[27]  David S. Goodsell,et al.  RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy , 2018, Nucleic Acids Res..

[28]  Chuan Wang,et al.  Expression signatures of exosomal long non-coding RNAs in urine serve as novel non-invasive biomarkers for diagnosis and recurrence prediction of bladder cancer , 2018, Molecular Cancer.

[29]  Astrid Gall,et al.  Ensembl 2020 , 2019, Nucleic Acids Res..

[30]  Marcel E. Dinger,et al.  lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs , 2014, Nucleic Acids Res..

[31]  Hecheng Zhou,et al.  CircRNA: functions and properties of a novel potential biomarker for cancer , 2017, Molecular Cancer.

[32]  Yuedong Yang,et al.  Predicting functional long non-coding RNAs validated by low throughput experiments , 2019, bioRxiv.

[33]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[34]  E. Lander,et al.  The NORAD lncRNA assembles a topoisomerase complex critical for genome stability , 2018, Nature.

[35]  Julio Vera,et al.  Exosomal lncRNAs and cancer: connecting the missing links , 2018, Bioinform..

[36]  S. Dimmeler,et al.  Long Noncoding RNAs in Cardiovascular Diseases , 2015, Circulation research.

[37]  Wei Wu,et al.  NONCODE 2016: an informative and valuable data source of long non-coding RNAs , 2015, Nucleic Acids Res..

[38]  Hong-yu Zhang,et al.  ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types , 2019, Nucleic Acids Res..

[39]  Zhen Yang,et al.  LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases , 2018, Nucleic Acids Res..

[40]  Yaoqi Zhou,et al.  EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments , 2017, Nucleic Acids Res..

[41]  Tao Liu,et al.  NONCODE v2.0: decoding the non-coding , 2007, Nucleic Acids Res..

[42]  M. Zhuang,et al.  Capturing RNA–protein interaction via CRUIS , 2020, Nucleic acids research.

[43]  Gong Zhang,et al.  A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma , 2018, Nature Communications.