NONCODEV5: a Comprehensive Annotation Database for Long Non-coding RNAs

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2017 Nov 16

PMID 29140524

Citations 275

Authors

Shuangsang Fang

Lili Zhang

Jincheng Guo

Yiwei Niu

Yang Wu

Hui Li

Lianhe Zhao

Xiyuan Li

Xueyi Teng

Xianhui Sun

Liang Sun

Michael Q Zhang

Runsheng Chen

Yi Zhao

Affiliations

Soon will be listed here.

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/.

Citing Articles

A heterogeneous information network learning model with neighborhood-level structural representation for predicting lncRNA-miRNA interactions.

Zhao B, Su X, Yang Y, Li D, Li G, Hu P Comput Struct Biotechnol J. 2025; 23:2924-2933.

PMID: 39963422 PMC: 11832017. DOI: 10.1016/j.csbj.2024.06.032.

LncRNA UCA1 regulates immune micro-environment in cisplatin-induced AKI by miRNA-4498/AKT3 pathway.

Hongjun P, Mukanhaire L, Zhen L, Ting W, Hongye L, Xiaotian Z PLoS One. 2025; 20(2):e0314654.

PMID: 39937792 PMC: 11819503. DOI: 10.1371/journal.pone.0314654.

RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models.

Asim M, Ibrahim M, Asif T, Dengel A Heliyon. 2025; 11(2):e41488.

PMID: 39897847 PMC: 11783440. DOI: 10.1016/j.heliyon.2024.e41488.

Modulating gene expression as a strategy to investigate thyroid cancer biology.

de Mello D, Menezes J, de Oliveira A, Cristovao M, Kimura E, Fuziwara C Arch Endocrinol Metab. 2025; 68(Spec Issue):e240073.

PMID: 39876973 PMC: 11771757. DOI: 10.20945/2359-4292-2024-0073.

ABCA1-Super Enhancer RNA Promotes Cholesterol Efflux, Reduces Macrophage-Mediated Inflammation and Atherosclerosis.

Wang J, Xiao Q, Cai Y, Wang M, Chen C, Wang L JACC Basic Transl Sci. 2025; 9(12):1388-1405.

PMID: 39822602 PMC: 11733767. DOI: 10.1016/j.jacbts.2024.08.005.

References

Xu T, Hu X, Liu X, Wang H, Lin K, Pan Y . Association between SNPs in Long Non-coding RNAs and the Risk of Female Breast Cancer in a Chinese Population. J Cancer. 2017; 8(7):1162-1169. PMC: 5463430. DOI: 10.7150/jca.18055. View

Weakley S, Wang H, Yao Q, Chen C . Expression and function of a large non-coding RNA gene XIST in human cancer. World J Surg. 2011; 35(8):1751-6. PMC: 3275083. DOI: 10.1007/s00268-010-0951-0. View

Wan Y, Qu K, Zhang Q, Flynn R, Manor O, Ouyang Z . Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 2014; 505(7485):706-9. PMC: 3973747. DOI: 10.1038/nature12946. View

Hindorff L, Sethupathy P, Junkins H, Ramos E, Mehta J, Collins F . Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009; 106(23):9362-7. PMC: 2687147. DOI: 10.1073/pnas.0903103106. View

Fu M, Zou C, Pan L, Liang W, Qian H, Xu W . Long noncoding RNAs in digestive system cancers: Functional roles, molecular mechanisms, and clinical implications (Review). Oncol Rep. 2016; 36(3):1207-18. DOI: 10.3892/or.2016.4929. View

Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman J . Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature. 2013; 505(7485):701-5. PMC: 3966492. DOI: 10.1038/nature12894. View

Altman R . PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Nat Genet. 2007; 39(4):426. PMC: 3203536. DOI: 10.1038/ng0407-426. View

Jin G, Sun J, Isaacs S, Wiley K, Kim S, Chu L . Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk. Carcinogenesis. 2011; 32(11):1655-9. PMC: 3204347. DOI: 10.1093/carcin/bgr187. View

Li Y, Zheng Q, Bao C, Li S, Guo W, Zhao J . Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis. Cell Res. 2015; 25(8):981-4. PMC: 4528056. DOI: 10.1038/cr.2015.82. View

10.

Robinson M, McCarthy D, Smyth G . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26(1):139-40. PMC: 2796818. DOI: 10.1093/bioinformatics/btp616. View

11.

Kopylova E, Noe L, Touzet H . SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012; 28(24):3211-7. DOI: 10.1093/bioinformatics/bts611. View

12.

Yates A, Akanni W, Amode M, Barrell D, Billis K, Carvalho-Silva D . Ensembl 2016. Nucleic Acids Res. 2015; 44(D1):D710-6. PMC: 4702834. DOI: 10.1093/nar/gkv1157. View

13.

Pennisi E . Shining a light on the genome's 'dark matter'. Science. 2010; 330(6011):1614. DOI: 10.1126/science.330.6011.1614. View

14.

Kerpedjiev P, Hammer S, Hofacker I . Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinformatics. 2015; 31(20):3377-9. PMC: 4595900. DOI: 10.1093/bioinformatics/btv372. View

15.

Sun Y, Wei G, Luo H, Wu W, Skogerbo G, Luo J . The long noncoding RNA SNHG1 promotes tumor growth through regulating transcription of both local and distal genes. Oncogene. 2017; 36(49):6774-6783. DOI: 10.1038/onc.2017.286. View

16.

Qureshi I, Mehler M . Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci. 2012; 13(8):528-41. PMC: 3478095. DOI: 10.1038/nrn3234. View

17.

Ma L, Li A, Zou D, Xu X, Xia L, Yu J . LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res. 2014; 43(Database issue):D187-92. PMC: 4383965. DOI: 10.1093/nar/gku1167. View

18.

Wang J, Cao Y, Zhang H, Wang T, Tian Q, Lu X . NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases. Nucleic Acids Res. 2016; 45(D1):D902-D907. PMC: 5210534. DOI: 10.1093/nar/gkw1038. View

19.

Tsai M, Manor O, Wan Y, Mosammaparast N, Wang J, Lan F . Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010; 329(5992):689-93. PMC: 2967777. DOI: 10.1126/science.1192002. View

20.

Mailman M, Feolo M, Jin Y, Kimura M, Tryka K, Bagoutdinov R . The NCBI dbGaP database of genotypes and phenotypes. Nat Genet. 2007; 39(10):1181-6. PMC: 2031016. DOI: 10.1038/ng1007-1181. View