LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases

Nucleic Acids Research - Tập 47 Số D1 - Trang D1034-D1037 - 2019
Zhenyu Bao1, Zhen Yang2, Zhou Huang1, Yiran Zhou1, Qinghua Cui3,1, Dong Dong4
1Department of Biomedical Informatics, School of Basic Medical Sciences, MOE Key Lab of Cardiovascular Sciences, Center for Noncoding RNA Medicine, Peking University, Beijing 100190, China
2Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
3Center of Bioinformatics, Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
4Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China

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Tài liệu tham khảo

Lalevee, 2015, Long noncoding RNAs in human disease: emerging mechanisms and therapeutic strategies, Epigenomics, 7, 877, 10.2217/epi.15.55

Wapinski, 2011, Long noncoding RNAs and human disease, Trends Cell Biol., 21, 354, 10.1016/j.tcb.2011.04.001

Mercer, 2013, Structure and function of long noncoding RNAs in epigenetic regulation, Nat. Struct. Mol. Biol., 20, 300, 10.1038/nsmb.2480

Schmitz, 2016, Mechanisms of long noncoding RNA function in development and disease, Cell. Mol. Life Sci., 73, 2491, 10.1007/s00018-016-2174-5

Chen, 2017, Long non-coding RNAs and complex diseases: from experimental results to computational models, Brief. Bioinform., 18, 558

Chen, 2013, LncRNADisease: a database for long-non-coding RNA-associated diseases, Nucleic Acids Res., 41, D983, 10.1093/nar/gks1099

He, 2018, Statistical analysis of non-coding RNA data, Cancer Lett., 417, 161, 10.1016/j.canlet.2017.12.029

Guo, 2016, Advances in long noncoding RNAs: identification, structure prediction and function annotation, Brief. Functi. Genomics, 15, 38, 10.1093/bfgp/elv022

Kibbe, 2015, Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data, Nucleic Acids Res., 43, D1071, 10.1093/nar/gku1011

Bhattacharya, 2011, MeSH: a window into full text for document summarization, Bioinformatics, 27, i120, 10.1093/bioinformatics/btr223

Memczak, 2013, Circular RNAs are a large class of animal RNAs with regulatory potency, Nature, 495, 333, 10.1038/nature11928

Li, 2018, Genome-wide identification of circular RNAs as a novel class of putative biomarkers for an ocular surface disease, Cell. Physiol. Biochem, 47, 1630, 10.1159/000490982

Pan, 2015, PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features, Mol. Biosyst., 11, 2219, 10.1039/C5MB00214A

Ning, 2016, Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers, Nucleic Acids Res., 44, D980, 10.1093/nar/gkv1094

Quek, 2015, lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs, Nucleic Acids Res., 43, D168, 10.1093/nar/gku988

Wang, 2017, NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases, Nucleic Acids Res., 45, D902, 10.1093/nar/gkw1038

Chen, 2013, Novel human lncRNA-disease association inference based on lncRNA expression profiles, Bioinformatics, 29, 2617, 10.1093/bioinformatics/btt426

Lan, 2017, LDAP: a web server for lncRNA-disease association prediction, Bioinformatics, 33, 458, 10.1093/bioinformatics/btw639

Sun, 2014, Inferring novel lncRNA-disease associations based on a random walk model of a lncRNA functional similarity network, Mol. Biosyst., 10, 2074, 10.1039/C3MB70608G

Wang, 2016, LncDisease: a sequence based bioinformatics tool for predicting lncRNA-disease associations, Nucleic Acids Res., 44, e90, 10.1093/nar/gkw093

Chou, 2016, miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database, Nucleic Acids Res., 44, D239, 10.1093/nar/gkv1258

Veres, 2015, ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis, Nucleic Acids Res., 43, D485, 10.1093/nar/gku1007

Kuhn, 2014, STITCH 4: integration of protein-chemical interactions with user data, Nucleic Acids Res., 42, D401, 10.1093/nar/gkt1207

Zhou, 2015, Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network, Mol. Biosyst., 11, 760, 10.1039/C4MB00511B

Kozomara, 2014, miRBase: annotating high confidence microRNAs using deep sequencing data, Nucleic Acids Res., 42, D68, 10.1093/nar/gkt1181

Kertesz, 2007, The role of site accessibility in microRNA target recognition, Nat. Genet., 39, 1278, 10.1038/ng2135

John, 2004, Human MicroRNA targets, PLoS Biol., 2, e363, 10.1371/journal.pbio.0020363

Kruger, 2006, RNAhybrid: microRNA target prediction easy, fast and flexible, Nucleic Acids Res., 34, W451, 10.1093/nar/gkl243

Zhou, 2018, EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments, Nucleic Acids Res., 46, D100, 10.1093/nar/gkx677