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NONCODE 2016: an informative and valuable data source of long non-coding RNAs
Open accessAbstract
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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“One of the major benefits of RNA-seq is that it quantifies the expression of the over 70 000 non-coding RNAs not usually measured with microarrays [1]”
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Additional file 13 of Identification of the conserved long non-coding RNAs in myogenesis
Bhattacharya, A., Champramary, S., Tripathi, T., Thakur, D., Ioshikhes, I. P., Singh, S. K., & Nandi, S. (2021) · Figshare · doi:10.6084/m9.figshare.14570195
Additional file 5 of Identification of the conserved long non-coding RNAs in myogenesis
Bhattacharya, A., Champramary, S., Tripathi, T., Thakur, D., Ioshikhes, I. P., Singh, S. K., & Nandi, S. (2021) · Figshare · doi:10.6084/m9.figshare.14570219
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Additional file 3 of Identification of the conserved long non-coding RNAs in myogenesis
Bhattacharya, A., Champramary, S., Tripathi, T., Thakur, D., Ioshikhes, I. P., Singh, S. K., & Nandi, S. (2021) · Figshare · doi:10.6084/m9.figshare.14570213
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Additional file 12 of Identification of the conserved long non-coding RNAs in myogenesis
Bhattacharya, A., Champramary, S., Tripathi, T., Thakur, D., Ioshikhes, I. P., Singh, S. K., & Nandi, S. (2021) · Figshare · doi:10.6084/m9.figshare.14570192
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Additional file 16 of Identification of the conserved long non-coding RNAs in myogenesis
Bhattacharya, A., Champramary, S., Tripathi, T., Thakur, D., Ioshikhes, I. P., Singh, S. K., & Nandi, S. (2021) · Figshare · doi:10.6084/m9.figshare.14570204
Additional file 1 of Identification of the conserved long non-coding RNAs in myogenesis
Bhattacharya, A., Champramary, S., Tripathi, T., Thakur, D., Ioshikhes, I. P., Singh, S. K., & Nandi, S. (2021) · Figshare · doi:10.6084/m9.figshare.14570207
Additional file 4 of Identification of the conserved long non-coding RNAs in myogenesis
Bhattacharya, A., Champramary, S., Tripathi, T., Thakur, D., Ioshikhes, I. P., Singh, S. K., & Nandi, S. (2021) · Figshare · doi:10.6084/m9.figshare.14570216
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Metadata
- 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
- 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
- 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
- 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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