The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
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/.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Figures
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]”
From Gene co-expression analysis for functional classification and gene–disease predictions (2017) · cites this paper as [1]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,145
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
Gupta, R. A., Shah, N., Wang, K., Kim, J., Horlings, H. M., Wong, D. J., Tsai, M.-C., Hung, T., Argani, P., Rinn, J. L., et al. (2010) · Nature · doi:10.1038/nature08975 · Cited by 5,205
Landscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187
Derrien, T., Johnson, R., Bussotti, G., Andrea Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,135
Molecular Mechanisms of Long Noncoding RNAs
Wang, K., & Chang, H. Y. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.018 · Cited by 4,462
Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X. H., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P., Segal, E., et al. (2007) · Cell · doi:10.1016/j.cell.2007.05.022 · Cited by 4,246
Evolution and Functions of Long Noncoding RNAs
Ponting, C. P., Oliver, P. L., & Reik, W. (2009) · Cell · doi:10.1016/j.cell.2009.02.006 · Cited by 4,208
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature · doi:10.1038/nature07672 · Cited by 4,098
Cabili, M. N., Trapnell, C., Goff, L. A., Koziol, M. J., Tazón‐Vega, B., Regev, A., & Rinn, J. L. (2011) · Genes & Development · doi:10.1101/gad.17446611 · Cited by 3,551
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
Tsai, M.-C., Manor, O., Wan, Y., Mosammaparast, N., Wang, J. K., Lan, F., Shi, Y., Segal, E., & Chang, H. Y. (2010) · Science · doi:10.1126/science.1192002 · Cited by 3,290
Cited by
Sorted by citations
Functional Classification and Experimental Dissection of Long Noncoding RNAs
Kopp, F. B., & Mendell, J. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.011 · Cited by 3,574
Lowe, R. G. T., Shirley, N. J., Bleackley, M. R., Dolan, S., & Shafee, T. M. A. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005457 · Cited by 1,307
Gene co-expression analysis for functional classification and gene–disease predictions
van Dam, S., Võsa, U., van der Graaf, A., Franke, L., & de Magalhães, J. P. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbw139 · Cited by 995
Hou, Y., Guo, H., Cao, C., Li, X., Hu, B., Zhu, P., Wu, X., Wen, L., Tang, F., Huang, Y., et al. (2016) · Cell Research · doi:10.1038/cr.2016.23 · Cited by 647
Long Non-Coding RNAs in the Regulation of Gene Expression: Physiology and Disease
Fernandes, J. C. R., Acuña, S. M., Aoki, J. I., Floeter‐Winter, L. M., & Muxel, S. M. (2019) · Non-Coding RNA · doi:10.3390/ncrna5010017 · Cited by 667
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
