Cited by 678Cancer-related molecular mechanisms researchGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

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NONCODE 2016: an informative and valuable data source of long non-coding RNAs

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Zhao, Yi, Li, Hui, Fang, Shuangsang, Kang, Yue, wu, Wei, Hao, Yajing, Li, Ziyang, Bu, Dechao, Sun, Ninghui, Zhang, Michael Q., Chen, Runsheng·2016·Nucleic Acids Research

DOI 10.1093/nar/gkv1252PMC PMC4702886

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Abstract

NONCODE (http://www.bioinfo.org/noncode/) is an interactive database that aims to present the most complete collection and annotation of non-coding RNAs, especially long non-coding RNAs (lncRNAs). The recently reduced cost of RNA sequencing has produced an explosion of newly identified data. Revolutionary third-generation sequencing methods have also contributed to more accurate annotations. Accumulative experimental data also provides more comprehensive knowledge of lncRNA functions. In this update, NONCODE has added six new species, bringing the total to 16 species altogether. The lncRNAs in NONCODE have increased from 210 831 to 527,336. For human and mouse, the lncRNA numbers are 167,150 and 130,558, respectively. NONCODE 2016 has also introduced three important new features: (i) conservation annotation; (ii) the relationships between lncRNAs and diseases; and (iii) an interface to choose high-quality datasets through predicted scores, literature support and long-read sequencing method support. NONCODE is also accessible through http://www.noncode.org/.

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Figure 1. Disease related data acquisition pipelineCC BY-NC · PubMed Central

Figure 2. Conservation annotation for NONHSAG200087.CC BY-NC · PubMed Central

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Additional file 10 of FishDB: an integrated functional genomics database for fishes
Yang, L., Xu, Z., Zeng, H., Sun, N., Wu, B., Wang, C., Jing, B., Li, L., Dong, Y., & He, S. (2020) · Figshare · doi:10.6084/m9.figshare.13251071
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Additional file 4 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189691
Additional file 1 of FishDB: an integrated functional genomics database for fishes
Yang, L., Xu, Z., Zeng, H., Sun, N., Wu, B., Wang, C., Jing, B., Li, L., Dong, Y., & He, S. (2020) · Figshare · doi:10.6084/m9.figshare.13251074
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Additional file 8 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189703
Additional file 6 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189697
Additional file 4 of FishDB: an integrated functional genomics database for fishes
Yang, L., Xu, Z., Zeng, H., Sun, N., Wu, B., Wang, C., Jing, B., Li, L., Dong, Y., & He, S. (2020) · Figshare · doi:10.6084/m9.figshare.13251083
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Additional file 7 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189700
Additional file 10 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189631
Additional file 18 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189658
Additional file 2 of FishDB: an integrated functional genomics database for fishes
Yang, L., Xu, Z., Zeng, H., Sun, N., Wu, B., Wang, C., Jing, B., Li, L., Dong, Y., & He, S. (2020) · Figshare · doi:10.6084/m9.figshare.13251077
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Additional file 9 of FishDB: an integrated functional genomics database for fishes
Yang, L., Xu, Z., Zeng, H., Sun, N., Wu, B., Wang, C., Jing, B., Li, L., Dong, Y., & He, S. (2020) · Figshare · doi:10.6084/m9.figshare.13251098
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Additional file 11 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189634
Additional file 3 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189688
Additional file 19 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189661
Additional file 13 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189640
Additional file 6 of FishDB: an integrated functional genomics database for fishes
Yang, L., Xu, Z., Zeng, H., Sun, N., Wu, B., Wang, C., Jing, B., Li, L., Dong, Y., & He, S. (2020) · Figshare · doi:10.6084/m9.figshare.13251089
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Additional file 7 of FishDB: an integrated functional genomics database for fishes
Yang, L., Xu, Z., Zeng, H., Sun, N., Wu, B., Wang, C., Jing, B., Li, L., Dong, Y., & He, S. (2020) · Figshare · doi:10.6084/m9.figshare.13251092
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Additional file 12 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189637
Additional file 20 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189667
Additional file 22 of Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics
Hou, L., Xie, J. H., Wu, Y., Wang, J., Duan, A., Ao, Y., Liu, X., Yu, X., Yan, H., Perreault, J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14189673

Authors: Zhao, Y., Li, H., Fang, S., Kang, Y., wu, W., Hao, Y., Li, Z., Bu, D., Sun, N., Zhang, M. Q., & Chen, R.
Affiliations: Tsinghua University (CN)
Chinese Academy of Sciences (CN)
Corresponding author: Chen, Runsheng
ORCID: Zhao, Yi
Li, Hui
Kang, Yue
wu, Wei
Hao, Yajing
Li, Ziyang
Bu, Dechao
Sun, Ninghui
Zhang, Michael Q.
Chen, Runsheng
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2015-11-19
Volume: 44
Issue: D1
Pages: D203-D208
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkv1252
PMC: PMC4702886
OpenAlex: W2174181728
Cited by: 643
References: 47
Citations by year: 2026: 15 · 2025: 22 · 2024: 37 · 2023: 44 · 2022: 50 · 2021: 95 · 2020: 77 · 2019: 75 · 2018: 99 · 2017: 76 · 2016: 51
FWCI: 25.24
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/4.0/ (vor, 362 d)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: National Natural Science Foundation of China (31371320, 31401119, 91229120)
Major Research Plan
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Keywords: long non-coding RNA, lncRNA annotation, lncRNA conservation, lncRNA function, RNA sequencing data, long-read sequencing, species expansion
MeSH terms: Animals, Base Sequence, Cattle, Disease, Humans, Conserved Sequence, Databases, Nucleic Acid, Mice, Rats, Molecular Sequence Annotation, RNA, Long Noncoding

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