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/.
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
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?
RNA-seq quantifies the expression of over 70 000 non-coding RNAs not usually measured with microarrays.
“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]
The Introduction says RNA sequencing has led to the identification of many long non-coding RNAs, and Data Collection and Processing describes expression profiles for them (page numbers unavailable). The paper does not say RNA-seq quantifies the expression of over 70,000 non-coding RNAs or compare its coverage with microarrays; its database counts are not counts of RNAs whose expression RNA-seq quantified. (LLM, conf=0.82)
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.
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 11,930 · see citing works
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 5,203 · see citing works
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 · see citing works
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 5,017 · see citing works
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 4,917 · see citing works
Molecular Mechanisms of Long Noncoding RNAs
Wang, K., & Chang, H. Y. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.018 · Cited by 4,390 · see citing works
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 · see citing works
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 · see citing works
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 3,473 · see citing works
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 · see citing works
The landscape of long noncoding RNAs in the human transcriptome
Iyer, M. K., Niknafs, Y. S., Malik, R., Singhal, U., Sahu, A., Hosono, Y., Barrette, T. R., Prensner, J. R., Evans, J. R., Zhao, S., et al. (2015) · Nature Genetics · doi:10.1038/ng.3192 · Cited by 2,738 · see citing works
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1229 · Cited by 2,707 · see citing works
lincRNAs: Genomics, Evolution, and Mechanisms
Ulitsky, I., & Bartel, D. P. (2013) · Cell · doi:10.1016/j.cell.2013.06.020 · Cited by 2,596 · see citing works
Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts
Sun, L. D., Luo, H., Bu, D., Zhao, G., Yu, K., Zhang, C., Liu, Y., Chen, R., & Zhao, Y. C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt646 · Cited by 2,110 · see citing works
Self-citationlincRNAs act in the circuitry controlling pluripotency and differentiation
Guttman, M., Donaghey, J., Carey, B. W., Garber, M. G., Grenier, J. K., Munson, G., Young, G., Lucas, A. B., Ach, R. A., Bruhn, L., et al. (2011) · Nature · doi:10.1038/nature10398 · Cited by 1,845 · see citing works
The evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., et al. (2011) · Nature · doi:10.1038/nature10532 · Cited by 1,248 · see citing works
Human–Mouse Alignments with BLASTZPreprint
Schwartz, S., Kent, W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D. H., & Miller, W. (2002) · Genome Research · doi:10.1101/gr.809403 · Cited by 1,231 · see citing works
Cunningham, F., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1010 · Cited by 1,115 · see citing works
The evolution of lncRNA repertoires and expression patterns in tetrapods
Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J. C., Grützner, F., & Kaessmann, H. (2014) · Nature · doi:10.1038/nature12943 · Cited by 984 · see citing works
Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues
Merkin, J., Russell, C., Chen, P., & Burge, C. B. (2012) · Science · doi:10.1126/science.1228186 · Cited by 972 · see citing works
RefSeq: an update on mammalian reference sequences
Pruitt, K. D., Brown, G., Hiatt, S. M., Thibaud‐Nissen, F., Astashyn, A., Ermolaeva, O. D., Farrell, C. M., Hart, J. A., Landrum, M., McGarvey, K. M., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1114 · Cited by 936 · see citing works
Self-citationFunctionality or transcriptional noise? Evidence for selection within long noncoding RNAsPreprint
Ponjavic, J., Ponting, C. P., & Lunter, G. A. (2007) · Genome Research · doi:10.1101/gr.6036807 · Cited by 731 · see citing works
A single-molecule long-read survey of the human transcriptome
Sharon, D., Tilgner, H., Grubert, F., & Snyder, M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2705 · Cited by 701 · see citing works
Assessment of transcript reconstruction methods for RNA-seq
The RGASP Consortium, Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Hubbard, T. J., Guigó, R., Harrow, J., & Bertone, P. (2013) · Nature Methods · doi:10.1038/nmeth.2714 · Cited by 699 · see citing works
Liao, Q., Liu, C., Yuan, X., Kang, S., Miao, R., Xiao, H., Zhao, G., Luo, H., Bu, D., Zhao, H., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1348 · Cited by 557 · see citing works
Self-citationlncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
Quek, X. C., Thomson, D. W., Mååg, J. L. V., Bartoniček, N., Signal, B., Clark, M. B., Gloss, B., & Dinger, M. E. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku988 · Cited by 529 · see citing works
NONCODE v3.0: integrative annotation of long noncoding RNAs
Bu, D., Yu, K., Sun, S., Xie, C., Skogerbø, G., Miao, R., Xiao, H., Liao, Q., Luo, H., Zhao, G., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1175 · Cited by 411 · see citing works
Self-citationNONCODEv4: exploring the world of long non-coding RNA genes
Xie, C., Yuan, J., Li, H., Li, M., Zhao, G., Bu, D., Zhu, W., Wu, W., Chen, R., & Zhao, Y. C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1222 · Cited by 401 · see citing works
Self-citationAn update on LNCipedia: a database for annotated human lncRNA sequences
Volders, P., Verheggen, K., Menschaert, G., Vandepoele, K., Martens, L., Vandesompele, J., & Mestdagh, P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1060 · Cited by 355 · see citing works
The UCSC Genome Browser database: extensions and updates 2011
Dreszer, T. R., Karolchik, D., Zweig, A. S., Hinrichs, A. S., Raney, B. J., Kuhn, R. M., Meyer, L. R., Wong, M., Sloan, C. A., Rosenbloom, K. R., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1055 · Cited by 349 · see citing works
NONCODE: an integrated knowledge database of non-coding RNAs
Liu, C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki041 · Cited by 324 · see citing works
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
Marques, A. C., & Ponting, C. P. (2009) · Genome biology · doi:10.1186/gb-2009-10-11-r124 · Cited by 255 · see citing works
lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse
Gong, J., Liu, W., Zhang, J., Miao, X., & Guo, A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1000 · Cited by 217 · see citing works
Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks
Guo, X., Gao, L., Liao, Q., Xiao, H., Ma, X., Yang, X., Luo, H., Zhao, G., Bu, D., Jiao, F., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks967 · Cited by 193 · see citing works
Self-citationNPInter v2.0: an updated database of ncRNA interactions
Yuan, J., Wu, W., Xie, C., Zhao, G., Zhao, Y. C., & Chen, R. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1057 · Cited by 184 · see citing works
Self-citationExpression and Function of a Large Non‐coding RNA Gene XIST in Human Cancer
Weakley, S. M., Wang, H., Yao, Q. C., & Chen, C. (2011) · World Journal of Surgery · doi:10.1007/s00268-010-0951-0 · Cited by 152 · see citing works
An update on LNCipedia: a database for annotated human lncRNA sequences
Volders, P. J., Verheggen, K., Menschaert, G., Vandepoele, K., Martens, L., Vandesompele, J., & Mestdagh, P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv295 · Cited by 140 · see citing works
NONCODE v2.0: decoding the non-coding
He, S., Liu, C., Skogerbø, G., Zhao, H., Wang, J., Liu, T., Bai, B., Zhao, Y., & Chen, R. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1011 · Cited by 130 · see citing works
Self-citationlncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs
Park, C., Yu, N., Choi, I., Kim, W., & Lee, S. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu325 · Cited by 129 · see citing works
LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs
Ma, L., Li, A., Zou, D., Xu, X., Xia, L., Yu, J. M., Bajić, V. B., & Zhang, Z. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1167 · Cited by 124 · see citing works
ncFANs: a web server for functional annotation of long non-coding RNAs
Liao, Q., Xiao, H., Bu, D., Xie, C., Miao, R., Luo, H., Zhao, G., Yu, K., Zhao, H., Skogerbø, G., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr432 · Cited by 119 · see citing works
Self-citationClustered microRNAs' coordination in regulating protein-protein interaction network
Yuan, X., Liu, C., Yang, P., He, S., Liao, Q., Kang, S., & Zhao, Y. C. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-65 · Cited by 118 · see citing works
Self-citationNPInter: the noncoding RNAs and protein related biomacromolecules interaction database
Wu, T. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj025 · Cited by 105 · see citing works
Ishikawa, K. (2005) · Nucleic Acids Research · doi:10.1093/nar/gni113 · Cited by 87 · see citing works
Shining a Light on the Genome's 'Dark Matter'
Pennisi, E. (2010) · Science · doi:10.1126/science.330.6011.1614 · Cited by 52 · see citing works
Evolutionary annotation of conserved long non-coding RNAs in major mammalian species
Bu, D., Luo, H., Jiao, F., Fang, S., Tan, C., Liu, Z., & Zhao, Y. C. (2015) · Science China Life Sciences · doi:10.1007/s11427-015-4881-9 · Cited by 32 · see citing works
Self-citationantiCODE: a natural sense-antisense transcripts database
Yin, Y., Zhao, Y. C., Wang, J., Liu, C., Chen, S., Chen, R., & Zhao, H. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-319 · Cited by 30 · see citing works
Self-citation
Flagged first, then by citations
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 3,522 · see citing works
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 1,186 · see citing works
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 1,086 · see citing works
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 · see citing works
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 647 · see citing works
Long non-coding RNAs and complex diseases: from experimental results to computational models
Chen, X., Yan, C. C., Zhang, X., & You, Z. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw060 · Cited by 568 · see citing works
NONCODEV5: a comprehensive annotation database for long non-coding RNAs
Fang, S., Zhang, L., Guo, J., Niu, Y., Wu, Y., Li, H., Zhao, L., Li, X., Teng, X., Sun, X., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1107 · Cited by 548 · see citing works
Self-citationThe BIG Data Center: from deposition to integration to translation
BIG Data Center Members (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1060 · Cited by 515 · see citing works
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome
Wucher, V., Legeai, F., Hédan, B., Rizk, G., Lagoutte, L., Leeb, T., Jagannathan, V., Cadieu, É., David, A., Lohi, H., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1306 · Cited by 461 · see citing works
Long Noncoding RNAs as Biomarkers in Cancer
Bolha, L., Ravnik‐Glavač, M., & Glavač, D. (2017) · Disease Markers · doi:10.1155/2017/7243968 · Cited by 367 · see citing works
Zhao, L., Wang, J., Li, Y., Song, T., Wu, Y., Fang, S., Bu, D., Li, H., Sun, L. D., Pei, D., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1046 · Cited by 327 · see citing works
Self-citationlncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs
Miao, Y., Liu, W., Zhang, Q., & Guo, A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1004 · Cited by 281 · see citing works
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Lagarde, J., Uszczyńska-Ratajczak, B., Carbonell, S., Pérez-Lluch, S., Abad, A., Davis, C., Gingeras, T., Frankish, A., Harrow, J., Guigó, R., et al. (2017) · Nature Genetics · doi:10.1038/ng.3988 · Cited by 265 · see citing works
Long Non-coding RNAs in Cancer: Implications for Diagnosis, Prognosis, and Therapy
Qian, Y., Shi, L., & Luo, Z. Y. (2020) · Frontiers in Medicine · doi:10.3389/fmed.2020.612393 · Cited by 260 · see citing works
RNAcentral: a comprehensive database of non-coding RNA sequences
Petrov, A. I., Kay, S., Kalvari, I., Howe, K., Gray, K. A., Bruford, E. A., Kersey, P. J., Cochrane, G., Finn, R. D., Bateman, A. G., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1008 · Cited by 258 · see citing works
Self-citationSallam, T., Jones, M., Thomas, B. J., Wu, X., Gilliland, T., Qian, K., Eskin, A., Casero, D., Zhang, Z., Sandhu, J., et al. (2018) · Nature Medicine · doi:10.1038/nm.4479 · Cited by 254 · see citing works
Long Noncoding RNA Discovery in Cardiovascular Disease
Sallam, T., Sandhu, J., & Tontonoz, P. (2018) · Circulation Research · doi:10.1161/circresaha.117.311802 · Cited by 252 · see citing works
Rizvi, A. H., Camara, P. G., Kandror, E. K., Roberts, T. J., Schieren, I., Maniatis, T., & Rabadan, R. (2017) · Nature Biotechnology · doi:10.1038/nbt.3854 · Cited by 248 · see citing works
Engineering salinity tolerance in plants: progress and prospects
Wani, S. H., Kumar, V., Khare, T., Guddimalli, R., Parveda, M., Solymosi, K., Suprasanna, P., & Kavi Kishor, P. B. (2020) · Planta · doi:10.1007/s00425-020-03366-6 · Cited by 233 · see citing works
Non-Coding RNAs and Their Roles in Stress Response in Plants
Wang, J., Meng, X., Dobrovolskaya, O. B., Orlov, Y. L., & Chen, M. (2017) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2017.01.007 · Cited by 239 · see citing works
Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation
Jha, U. C., Nayyar, H., Jha, R., Khurshid, M., Zhou, M., Mantri, N. L., & Siddique, K. H. M. (2020) · BMC Plant Biology · doi:10.1186/s12870-020-02595-x · Cited by 227 · see citing works
The New RNA World: Growing Evidence for Long Noncoding RNA Functionality
Jandura, A., & Krause, H. M. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.08.002 · Cited by 213 · see citing works
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search
Huang, L., Zhang, H., Deng, D., Zhao, K., Liu, K., Hendrix, D. A., & Mathews, D. H. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz375 · Cited by 207 · see citing works
“1, from the NONCODE database (Zhao et al., 2016)).”
Platforms for Investigating LncRNA Functions
Richard, J. L. C., & Eichhorn, P. J. A. (2018) · SLAS TECHNOLOGY · doi:10.1177/2472630318780639 · Cited by 187 · see citing works
Computational models for lncRNA function prediction and functional similarity calculation
Chen, X., Sun, Y., Guan, N., Qu, J., Huang, Z.-A., Zhu, Z., & Li, J. (2018) · Briefings in Functional Genomics · doi:10.1093/bfgp/ely031 · Cited by 188 · see citing works
Insect genomes: progress and challenges
Li, F., Zhao, X., Li, M., He, K., Huang, C., Zhou, Y., Li, Z., & Walters, J. R. (2019) · Insect Molecular Biology · doi:10.1111/imb.12599 · Cited by 178 · see citing works
Self-citationNoncoding RNAs in neurodegeneration
Salta, E., & De Strooper, B. (2017) · Nature Reviews Neuroscience · doi:10.1038/nrn.2017.90 · Cited by 183 · see citing works
Wang, H. V., & Chekanova, J. A. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-981-10-5203-3_5 · Cited by 173 · see citing works
Emerging roles of long non-coding RNAs in plant response to biotic and abiotic stresses
Nejat, N., & Mantri, N. L. (2017) · Critical Reviews in Biotechnology · doi:10.1080/07388551.2017.1312270 · Cited by 171 · see citing works
The non-coding RNA landscape of human hematopoiesis and leukemia
Schwarzer, A., Emmrich, S., Schmidt, F., Beck, D., Ng, M. S. W., Reimer, C., Adams, F. F., Grasedieck, S., Witte, D., Käbler, S., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00212-4 · Cited by 156 · see citing works
Sex-Specific Role for the Long Non-coding RNA LINC00473 in Depression
Issler, O., van der Zee, Y. Y., Ramakrishnan, A., Wang, J., Tan, C., Loh, Y.-H. E., Purushothaman, I., Walker, D. M., Lorsch, Z. S., Hamilton, P. J., et al. (2020) · Neuron · doi:10.1016/j.neuron.2020.03.023 · Cited by 156 · see citing works
Long non-coding RNAs as prognostic markers in human breast cancer
Liu, H., Li, J., Koirala, P., Ding, X., Chen, B., Wang, Y., Wang, Z., Wang, C., Zhang, X., & Mo, Y.-Y. (2016) · Oncotarget · doi:10.18632/oncotarget.7828 · Cited by 155 · see citing works
POSTAR2: deciphering the post-transcriptional regulatory logics
Zhu, Y., Xu, G., Yang, Y., Xu, Z., Chen, X., Shi, B., Xie, D., Lu, Z. J., & Wang, P. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky830 · Cited by 152 · see citing works
cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs
Fehlmann, T., Reinheimer, S., Geng, C., Su, X., Drmanac, S., Alexeev, A., Zhang, C., Backes, C., Ludwig, N., Hart, M., et al. (2016) · Clinical Epigenetics · doi:10.1186/s13148-016-0287-1 · Cited by 150 · see citing works
Long noncoding RNA expression profiling in cancer: Challenges and opportunities
Lorenzi, L., Cobos, F. A., Decock, A., Everaert, C., Helsmoortel, H. H., Lefever, S., Verboom, K., Volders, P., Speleman, F., Vandesompele, J., et al. (2018) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22709 · Cited by 150 · see citing works
Characterization and identification of long non-coding RNAs based on feature relationship
Wang, G., Yin, H., Li, B., Yu, C., Wang, F., Xu, X., Cao, J., Bào, Y., Wang, L., Abbasi, A. A., et al. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz008 · Cited by 146 · see citing works
“Cat’s Cradling” the 3D Genome by the Act of LncRNA Transcription
Melé, M., & Rinn, J. L. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.011 · Cited by 143 · see citing works
Liu, X., Li, D., Zhang, D., Yin, D., Zhao, Y. C., Ji, C., Zhao, X. F., Li, X., He, Q., Chen, R., et al. (2018) · New Phytologist · doi:10.1111/nph.15023 · Cited by 140 · see citing works
Self-citationClassification and experimental identification of plant long non-coding RNAs
Rai, M. I., Alam, M., Lightfoot, D. A., Gurha, P., & Afzal, A. J. (2018) · Genomics · doi:10.1016/j.ygeno.2018.04.014 · Cited by 140 · see citing works
LNCediting: a database for functional effects of RNA editing in lncRNAs
Gong, J., Liu, C., Liu, W., Xiang, Y., Diao, L., Guo, A., & Han, L. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw835 · Cited by 137 · see citing works
Amaral, P., Leonardi, T., Han, N., Viré, E. A., Gascoigne, D. K., Arias‐Carrasco, R., Büscher, M., Pandolfini, L., Zhang, A., Pluchino, S., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1405-5 · Cited by 134 · see citing works
Long noncoding RNA: a crosslink in biological regulatory network
Zhang, Y.-W., Yang, T., & Liao, Q. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx042 · Cited by 134 · see citing works
Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
Stojic, L., Lun, A. T. L., Mangei, J., Mascalchi, P., Quarantotti, V., Barr, A. R., Bakal, C., Marioni, J. C., Gergely, F. V., & Odom, D. T. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky437 · Cited by 131 · see citing works
Huang, Y., Chan, K. C. C., & You, Z. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx672 · Cited by 128 · see citing works
SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci
Hao, Y., Zhang, L., Niu, Y., Cai, T., Luo, J., He, S., Zhang, B., Zhang, D., Qin, Y., Yang, F., et al. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx005 · Cited by 125 · see citing works
Self-citationThe state of play in higher eukaryote gene annotation
Mudge, J. M., & Harrow, J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.119 · Cited by 122 · see citing works
Kumar, V., Khare, T. R., Shriram, V., & Wani, S. H. (2017) · Plant Cell Reports · doi:10.1007/s00299-017-2210-4 · Cited by 121 · see citing works
The lncRNA SLNCR1 Mediates Melanoma Invasion through a Conserved SRA1-like Region
Schmidt, K., Joyce, C. E., Buquicchio, F. A., Brown, A. S., Ritz, J., Distel, R. J., Yoon, C. H., & Novina, C. D. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.018 · Cited by 118 · see citing works
An expanded landscape of human long noncoding RNA
Jiang, S., Cheng, S., Ren, L., Wang, Q., Kang, Y.-J., Ding, Y., Hou, M. L., Yang, X., Lin, Y., Liang, N., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz621 · Cited by 114 · see citing works
Self-citationRegulatory variants: from detection to predicting impact
Rojano, E., Seoane, P., Ranea, J. A. G., & Perkins, J. R. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby039 · Cited by 110 · see citing works
Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs
Ribeiro, D. M., Zanzoni, A., Cipriano, A., Ponti, R. D., Spinelli, L., Ballarino, M., Bozzoni, I., Tartaglia, G. G., & Brun, C. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1169 · Cited by 108 · see citing works
LncRNAs Regulatory Networks in Cellular Senescence
Pavan Kumar, P. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20112615 · Cited by 107 · see citing works
Sun, Y., & Chen, Y.-Q. (2020) · Journal of Hematology & Oncology · doi:10.1186/s13045-020-00945-8 · Cited by 108 · see citing works
Zhao, J., Zhang, W., Lin, M., Wu, W., Jiang, P., Tou, E., Xue, M., Richards, A. F., Jourd’heuil, D., Asif, A., et al. (2016) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.116.307879 · Cited by 108 · see citing works
Self-citationGomes, C. P. C., Spencer, H., Ford, K. L., Michel, L. Y. M., Baker, A. H., Emanueli, C., Balligand, J., & Devaux, Y. (2017) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2017.07.014 · Cited by 108 · see citing works
Wang, X., Lan, Z., He, J., Lai, Q., Yao, X., Li, Q., Liu, Y., Lai, H., Gu, C.-C., Yan, Q., et al. (2019) · Cancer Cell International · doi:10.1186/s12935-019-0951-6 · Cited by 108 · see citing works
Role of Pseudogenes in Tumorigenesis
Hu, X., Yang, L., & Mo, Y. (2018) · Cancers · doi:10.3390/cancers10080256 · Cited by 106 · see citing works
Li, X. L., Pongor, L. S., Tang, W., Das, S., Muys, B. R., Jones, M. F., Lazar, S. B., Dangelmaier, E. A., Hartford, C. C. R., Grammatikakis, I., et al. (2020) · eLife · doi:10.7554/elife.53734 · Cited by 105 · see citing works
CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs
Szcześniak, M. W., Bryzghalov, O., Ciomborowska-Basheer, J., & Makałowska, I. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9045-0_26 · Cited by 104 · see citing works
Liu, S., Wang, Z., Chen, D., Zhang, B., Tian, R.-R., Wu, J., Zhang, Y., Xu, K., Yang, L.-M., Cheng, C., et al. (2017) · Genome Research · doi:10.1101/gr.217463.116 · Cited by 130 · see citing works
Long Non-Coding RNAs: A Novel Paradigm for Toxicology
Dempsey, J. L., & Cui, J. Y. (2016) · Toxicological Sciences · doi:10.1093/toxsci/kfw203 · Cited by 102 · see citing works
RNA Sequencing and Co-expressed Long Non-coding RNA in Modern and Wild Wheats
Cagirici, H. B., Alptekin, B., & Budak, H. (2017) · Scientific Reports · doi:10.1038/s41598-017-11170-8 · Cited by 100 · see citing works
Computational Approaches for Functional Prediction and Characterisation of Long Noncoding RNAs
Signal, B., Gloss, B., & Dinger, M. E. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.08.004 · Cited by 95 · see citing works
Dong, X., Liao, Z., Gritsch, D., Hadzhiev, Y., Bai, Y., Locascio, J. J., Guennewig, B., Liu, G., Blauwendraat, C., Wang, T., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0223-0 · Cited by 94 · see citing works
The role of long non-coding RNAs in rheumatic diseases
Tang, Y., Zhou, T., Yu, X., Xue, Z., & Shen, N. (2017) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2017.162 · Cited by 89 · see citing works
Downregulation of long non-coding RNA HCG11 predicts a poor prognosis in prostate cancer
Zhang, Y., Zhang, P., Wan, X., Su, X., Kong, Z., Zhai, Q., Xiang, X., Li, L., & Li, Y. (2016) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2016.08.013 · Cited by 85 · see citing works
Chen, H., Zhang, Z., Jiang, S., Li, R., Li, W., Zhao, C., Hong, H., Huang, X., Li, H., & Bo, X. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz072 · Cited by 81 · see citing works
Self-citationZhang, H., Zhang, L., Mathews, D. H., & Huang, L. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa460 · Cited by 83 · see citing works
Long noncoding RNA repertoire in chicken liver and adipose tissue
Muret, K., Klopp, C., Wucher, V., Esquerré, D., Legeai, F., Lecerf, F., Désert, C., Boutin, M., Jehl, F., Acloque, H., et al. (2017) · Genetics Selection Evolution · doi:10.1186/s12711-016-0275-0 · Cited by 79 · see citing works
Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers
Latgé, G., Poulet, C., Bours, V., Josse, C., & Jérusalem, G. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19010123 · Cited by 81 · see citing works
Chao, T., Zhang, Q., Li, Z., Tiwari, S. K., Qin, Y., Yau, E. H., Sánchez, A. B., Singh, G., Chang, K., Kaul, M., et al. (2019) · mBio · doi:10.1128/mbio.02016-19 · Cited by 80 · see citing works
Self-citationFeng, S., Xu, M., Liu, F., Cui, C., & Zhou, B. (2019) · BMC Plant Biology · doi:10.1186/s12870-019-1968-7 · Cited by 80 · see citing works
Non-Coding RNAs in Psychiatric Disorders and Suicidal Behavior
Yoshino, Y., & Dwivedi, Y. (2020) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2020.543893 · Cited by 82 · see citing works
Long non-coding RNA: Functional agent for disease traits
Jain, S., Thakkar, N., Chhatai, J., Bhadra, M. P., & Bhadra, U. (2016) · RNA Biology · doi:10.1080/15476286.2016.1172756 · Cited by 77 · see citing works
A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life
Umu, S. U., & Gardner, P. P. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw728 · Cited by 75 · see citing works
RBind: computational network method to predict RNA binding sites
Wang, K., Jian, Y., Wang, H., Zeng, C., & Zhao, Y. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty345 · Cited by 77 · see citing works
Self-citationThe 24th annualNucleic Acids Researchdatabase issue: a look back and upcoming changes
Galperin, M. Y., Fernández, X. M., & Rigden, D. J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1188 · Cited by 76 · see citing works
Gong, W., Song, Q., Ji, K., Gong, S., Wang, L., Chen, L., Zhang, J., & Yuan, D. (2020) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.0c05381 · Cited by 76 · see citing works
Petermann, F., Pękowska, A., Johnson, C., Jankovic, D. L., Shih, H., Jiang, K., Hudson, W. H., Brooks, S. R., Sun, H., Villarino, A. V., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.06.025 · Cited by 76 · see citing works
ncRNAs: New Players in Mitochondrial Health and Disease?
Gušić, M., & Prokisch, H. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00095 · Cited by 74 · see citing works
Mahpour, A., & Mullen, A. C. (2020) · JHEP Reports · doi:10.1016/j.jhepr.2020.100177 · Cited by 75 · see citing works
Zhou, B.-L., Zhao, H.-Y., Yu, J.-F., Guo, C., Dou, X.-H., Song, F., Hu, G.-D., Cao, Z.-X., Qu, Y., Yang, Y., et al. (2017) · Nucleic Acids Res. · doi:10.1093/nar/gkx677 · Cited by 67 · see citing works
Insights into the Functions of LncRNAs in Drosophila
Li, K., Tian, Y., Yuan, Y., Fan, X., Yang, M., He, Z., & Yang, D. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20184646 · Cited by 74 · see citing works
Tang, Z., Wu, Y., Yang, Y., Yang, Y., Wang, Z., Yuan, J., Yang, Y., Hua, C., Fan, X., Niu, G., et al. (2017) · Scientific Reports · doi:10.1038/srep43166 · Cited by 74 · see citing works
Wu, S., Liu, H., Huang, P.-J., Chang, I. Y., Lee, C., Yang, C.-Y., Tsai, W., & Tan, B. C. (2017) · GigaScience · doi:10.1093/gigascience/gix118 · Cited by 72 · see citing works
Zhou, B., Ji, B., Liu, K., Hu, G., Wang, F., Chen, Q., Ru, Y., Huang, P., Ren, J., Guo, C., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1076 · Cited by 72 · see citing works
Self-citationA comprehensive review of web-based non-coding RNA resources for cancer research
Zheng, Y., Liu, L., & Shukla, G. C. (2017) · Cancer Letters · doi:10.1016/j.canlet.2017.08.015 · Cited by 70 · see citing works
The cellular landscape of mid‐size noncoding RNA
Boivin, V., Faucher‐Giguère, L., Scott, M. S., & Elela, S. A. (2019) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1530 · Cited by 70 · see citing works
Present Scenario of Long Non-Coding RNAs in Plants
Bhatia, G., Goyal, N., Sharma, S., Upadhyay, S. K., & Singh, K. (2017) · Non-Coding RNA · doi:10.3390/ncrna3020016 · Cited by 68 · see citing works
Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants
Waseem, M., Liu, Y., & Xia, R. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms22010086 · Cited by 68 · see citing works
Insights into lncRNAs in Alzheimer’s disease mechanisms
Li, D., Zhang, J., Li, X., Chen, Y., Feng, Y., & Liu, Q. (2020) · RNA Biology · doi:10.1080/15476286.2020.1788848 · Cited by 66 · see citing works
Zhou, L., Ren, M., Zeng, T., Wang, W., Wang, X., Hu, M., Su, S., Sun, K., Wang, C., Liu, J., et al. (2019) · Cell Death and Disease · doi:10.1038/s41419-019-2047-6 · Cited by 65 · see citing works
Zhu, X., Wang, X., Wang, Y., & Zhao, Y. (2019) · Molecular Immunology · doi:10.1016/j.molimm.2019.11.009 · Cited by 65 · see citing works
Self-citationInvolvement of long noncoding RNAs in the pathogenesis of autoimmune diseases
Zou, Y., & Xu, H. (2020) · Journal of Translational Autoimmunity · doi:10.1016/j.jtauto.2020.100044 · Cited by 65 · see citing works
Molecular landscape of long noncoding RNAs in brain disorders
Yang, S., Lim, K., Kim, S.-H., & Joo, J. (2020) · Molecular Psychiatry · doi:10.1038/s41380-020-00947-5 · Cited by 66 · see citing works
The multifaceted actions of the lncRNA H19 in cardiovascular biology and diseases
Busscher, D., Boon, R. A., & Juni, R. P. (2022) · Clinical Science · doi:10.1042/cs20210994 · Cited by 65 · see citing works
Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs
Fehlmann, T., Backes, C., Kahraman, M., Haas, J., Ludwig, N., Posch, A. E., Würstle, M. L., Hübenthal, M., Franke, A., Meder, B., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx595 · Cited by 64 · see citing works
Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing
Li, F., Kaczor‐Urbanowicz, K. E., Sun, J. L., Majem, B., Lo, H.-C., Kim, Y., Koyano, K., Rao, S. L., Kang, S. Y., Kim, S. M., et al. (2018) · Clinical Chemistry · doi:10.1373/clinchem.2017.285072 · Cited by 64 · see citing works
Li, D., Tolleson, W. H., Yu, D., Chen, S., Guo, L., Xiao, W., Tong, W., & Ning, B. (2019) · Journal of Environmental Science and Health Part C · doi:10.1080/10590501.2019.1639481 · Cited by 64 · see citing works
Noncoding RNAs in Cardiac Hypertrophy
Li, Y., Liang, Y., Zhu, Y., Zhang, Y., & Bei, Y. (2018) · Journal of Cardiovascular Translational Research · doi:10.1007/s12265-018-9797-x · Cited by 63 · see citing works
- 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 › Agricultural and Biological Sciences › Plant Science › 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
