Cited by 555

An estimate of the total number of true human miRNAs

Alles, Julia, Fehlmann, Tobias, Fischer, Ulrike, Backes, Christina, Galata, Valentina, Minet, Marie, Hart, Martin, Abu-Halima, Masood +4 more·2019·Nucleic Acids Research

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gkz097

Cites

1 of 1 references verified0 citation errors · 0 not checkable

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.

A few free checks a day · papers already verified open instantly · results are public

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 current miRbase annotation of mammalian miRNA remains incomplete but can be readily expanded with the help of emerging small RNA-seq data.

    “We have recently demonstrated that the current miRbase annotation of mammalian miRNA remains incomplete but can be readily expanded with the help of emerging small RNA-seq data (46).”

    From A mouse tissue atlas of small noncoding RNA (2020) · cites this paper as [46]

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

Flagged first, then by citations

Research works printed but not linked: 53

  1. [1]Ambros V. The functions of animal microRNAs. Nature. 2004; 431: 350– 355. 15372042
  2. [2]Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116: 281– 297. 14744438
  3. [3]Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell. 2009; 136: 215– 233. 19167326 PMC3794896
  4. [4]Hart M., Nolte E., Wach S., Szczyrba J., Taubert H., Rau T.T., Hartmann A., Grasser F.A., Wullich B. Comparative microRNA profiling of prostate carcinomas with increasing tumor stage by deep sequencing. Mol. Cancer Res. 2014; 12: 250– 263. 24337069
  5. [5]Petriella D., De Summa S., Lacalamita R., Galetta D., Catino A., Logroscino A.F., Palumbo O., Carella M., Zito F.A., Simone G. et al. miRNA profiling in serum and tissue samples to assess noninvasive biomarkers for NSCLC clinical outcome. Tumour Biol. 2016; 37: 5503– 5513. 26566629
  6. [6]Drusco A., Nuovo G.J., Zanesi N., Di Leva G., Pichiorri F., Volinia S., Antenucci A., Costinean S., Bottoni A. et al. MicroRNA profiles discriminate among colon cancer metastasis. PLoS One. 2014; 9: e96670. 24921248 PMC4055753
  7. [7]Alles J., Menegatti J., Motsch N., Hart M., Eichner N., Reinhardt R., Meister G., Grasser F.A. miRNA expression profiling of Epstein-Barr virus-associated NKTL cell lines by Illumina deep sequencing. FEBS Open Bio. 2016; 6: 251– 263. PMC4821355 27239439
  8. [8]Wen Y., Han J., Chen J., Dong J., Xia Y., Liu J., Jiang Y., Dai J., Lu J., Jin G. et al. Plasma miRNAs as early biomarkers for detecting hepatocellular carcinoma. Int. J. Cancer. 2015; 137: 1679– 1690. 25845839
  9. [9]Akers J.C., Hua W., Li H., Ramakrishnan V., Yang Z., Quan K., Zhu W., Li J., Figueroa J., Hirshman B.R. et al. A cerebrospinal fluid microRNA signature as biomarker for glioblastoma. Oncotarget. 2017; 8: 68769– 68779. 28978155 PMC5620295
  10. [10]Abu-Halima M., Meese E., Keller A., Abdul-Khaliq H., Radle-Hurst T. Analysis of circulating microRNAs in patients with repaired Tetralogy of Fallot with and without heart failure. J. Transl. Med. 2017; 15: 156. 28693530 PMC5504636
  11. [11]Keller A., Meese E. Can circulating miRNAs live up to the promise of being minimal invasive biomarkers in clinical settings. Wiley Interdiscip. Rev. RNA. 2016; 7: 148– 156. 26670867
  12. [12]Ludwig N., Nourkami-Tutdibi N., Backes C., Lenhof H.P., Graf N., Keller A., Meese E. Circulating serum miRNAs as potential biomarkers for nephroblastoma. Pediatr. Blood Cancer. 2015; 62: 1360– 1367. 25787821
  13. [13]Abu-Halima M., Hammadeh M., Backes C., Fischer U., Leidinger P., Lubbad A.M., Keller A., Meese E. Panel of five microRNAs as potential biomarkers for the diagnosis and assessment of male infertility. Fertil. Steril. 2014; 102: 989– 997. 25108464
  14. [14]Leidinger P., Backes C., Deutscher S., Schmitt K., Mueller S.C., Frese K., Haas J., Ruprecht K., Paul F., Stahler C. et al. A blood based 12-miRNA signature of Alzheimer disease patients. Genome Biol. 2013; 14: R78. 23895045 PMC4053778
  15. [15]Keller A., Leidinger P., Bauer A., Elsharawy A., Haas J., Backes C., Wendschlag A., Giese N., Tjaden C., Ott K. et al. Toward the blood-borne miRNome of human diseases. Nat. Methods. 2011; 8: 841– 843. 21892151
  16. [16]Kozomara A., Birgaoanu M., Griffiths-Jones S. miRBase: from microRNA sequences to function. Nucleic Acids Res. 2018; 47: D155– D162. PMC6323917 30423142
  17. [17]Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 2004; 32: D109– D111. 14681370 PMC308757
  18. [18]Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011; 39: D152– D157. 21037258 PMC3013655
  19. [19]Kozomara A., Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014; 42: D68– D73. 24275495 PMC3965103
  20. [20]Backes C., Meder B., Hart M., Ludwig N., Leidinger P., Vogel B., Galata V., Roth P., Menegatti J., Grasser F. et al. Prioritizing and selecting likely novel miRNAs from NGS data. Nucleic Acids Res. 2016; 44: e53. 26635395 PMC4824081
  21. [21]Chiang H.R., Schoenfeld L.W., Ruby J.G., Auyeung V.C., Spies N., Baek D., Johnston W.K., Russ C., Luo S., Babiarz J.E. et al. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev. 2010; 24: 992– 1009. 20413612 PMC2867214
  22. [22]Meng Y., Shao C., Wang H., Chen M. Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants. RNA Biol. 2012; 9: 249– 253. 22336711
  23. [23]Wang X., Liu X.S. Systematic curation of miRBase annotation using integrated small RNA High-Throughput sequencing data for C. elegans and drosophila. Front. Genet. 2011; 2: 25. 22303321 PMC3268580
  24. [24]Hansen T.B., Kjems J., Bramsen J.B. Enhancing miRNA annotation confidence in miRBase by continuous cross dataset analysis. RNA Biol. 2011; 8: 378– 383. 21558790 PMC3218508
  25. [25]Brown M., Suryawanshi H., Hafner M., Farazi T.A., Tuschl T. Mammalian miRNA curation through next-generation sequencing. Front. Genet. 2013; 4: 145. 23935604 PMC3731538
  26. [26]Fromm B., Billipp T., Peck L.E., Johansen M., Tarver J.E., King B.L., Newcomb J.M., Sempere L.F., Flatmark K., Hovig E. et al. A uniform system for the annotation of vertebrate microRNA genes and the evolution of the human microRNAome. Annu. Rev. Genet. 2015; 49: 213– 242. 26473382 PMC4743252
  27. [27]Backes C., Fehlmann T., Kern F., Kehl T., Lenhof H.P., Meese E., Keller A. miRCarta: a central repository for collecting miRNA candidates. Nucleic Acids Res. 2017; 46: D160– D167. PMC5753177 29036653
  28. [28]Krawczak M., Reiss J., Schmidtke J., Rosler U. Polymerase chain reaction: replication errors and reliability of gene diagnosis. Nucleic Acids Res. 1989; 17: 2197– 2201. 2565023 PMC317589
  29. [29]Meyerhans A., Vartanian J.P., Wain-Hobson S. DNA recombination during PCR. Nucleic Acids Res. 1990; 18: 1687– 1691. 2186361 PMC330584
  30. [30]Friedlander M.R., Mackowiak S.D., Li N., Chen W., Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012; 40: 37– 52. 21911355 PMC3245920
  31. [31]Fehlmann T., Backes C., Alles J., Fischer U., Hart M., Kern F., Langseth H., Rounge T., Umu S.U., Kahraman M. et al. A high-resolution map of the human small non-coding transcriptome. Bioinformatics. 2017; 34: 1621– 1628. 29281000
  32. [32]Kodama Y., Shumway M., Leinonen R. International Nucleotide Sequence Database, C. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res. 2012; 40: D54– D56. 22009675 PMC3245110
  33. [33]Fehlmann T., Backes C., Kahraman M., Haas J., Ludwig N., Posch A.E., Wurstle M.L., Hubenthal M., Franke A., Meder B. et al. Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs. Nucleic Acids Res. 2017; 45: 8731– 8744. 28911107 PMC5587802
  34. [35]Keller A., Backes C., Haas J., Leidinger P., Maetzler W., Deuschle C., Berg D., Ruschil C., Galata V., Ruprecht K. et al. Validating Alzheimer's disease micro RNAs using next-generation sequencing. Alzheimers Dement. 2016; 12: 565– 576. 26806387
  35. [36]Graham F.L., Smiley J., Russell W.C., Nairn R. Characteristics of a human cell line transformed by DNA from human adenovirus type 5. J. Gen. Virol. 1977; 36: 59– 74. 886304
  36. [37]Thomas P., Smart T.G. HEK293 cell line: a vehicle for the expression of recombinant proteins. J. Pharmacol. Toxicol. Methods. 2005; 51: 187– 200. 15862464
  37. [38]Biasiolo M., Sales G., Lionetti M., Agnelli L., Todoerti K., Bisognin A., Coppe A., Romualdi C., Neri A., Bortoluzzi S. Impact of host genes and strand selection on miRNA and miRNA* expression. PLoS One. 2011; 6: e23854. 21909367 PMC3166117
  38. [39]Hu H.Y., Yan Z., Xu Y., Hu H., Menzel C., Zhou Y.H., Chen W., Khaitovich P. Sequence features associated with microRNA strand selection in humans and flies. BMC Genomics. 2009; 10: 413. 19732433 PMC2751786
  39. [40]Khvorova A., Reynolds A., Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell. 2003; 115: 209– 216. 14567918
  40. [41]Schamberger A., Sarkadi B., Orban T.I. Human mirtrons can express functional microRNAs simultaneously from both arms in a flanking exon-independent manner. RNA Biol. 2012; 9: 1177– 1185. 23018783 PMC3579885
  41. [42]Hube F., Ulveling D., Sureau A., Forveille S., Francastel C. Short intron-derived ncRNAs. Nucleic Acids Res. 2017; 45: 4768– 4781. 28053119 PMC5416886
  42. [43]Hansen T.B., Veno M.T., Jensen T.I., Schaefer A., Damgaard C.K., Kjems J. Argonaute-associated short introns are a novel class of gene regulators. Nat. Commun. 2016; 7: 11538. 27173734 PMC4869172
  43. [44]Magee R., Telonis A.G., Cherlin T., Rigoutsos I., Londin E. Assessment of isomiR discrimination using commercial qPCR methods. Noncoding RNA. 2017; 3: 18. 28730153 PMC5514785
  44. [45]Pillman K.A., Goodall G.J., Bracken C.P., Gantier M.P. miRNA length variation during macrophage stimulation confounds the interpretation of results: implications for miRNA quantification by RT-qPCR. RNA. 2019; 25: 232– 238. 30487268 PMC6348984
  45. [46]Nejad C., Pepin G., Behlke M.A., Gantier M.P. Modified polyadenylation-based RT-qPCR increases selectivity of amplification of 3′-MicroRNA isoforms. Front. Genet. 2018; 9: 11. 29416548 PMC5787544
  46. [47]Hou S., Fang M., Zhu Q., Liu Y., Liu L., Li X. MicroRNA-939 governs vascular integrity and angiogenesis through targeting gamma-catenin in endothelial cells. Biochem. Biophys. Res. Commun. 2017; 484: 27– 33. 28115160
  47. [48]Aghdaei F.H., Soltani B.M., Dokanehiifard S., Mowla S.J., Soleimani M. Overexpression of hsa-miR-939 follows by NGFR down-regulation and apoptosis reduction. J. Biosci. 2017; 42: 23– 30. 28229962
  48. [49]Zhang J.X., Xu Y., Gao Y., Chen C., Zheng Z.S., Yun M., Weng H.W., Xie D., Ye S. Decreased expression of miR-939 contributes to chemoresistance and metastasis of gastric cancer via dysregulation of SLC34A2 and Raf/MEK/ERK pathway. Mol. Cancer. 2017; 16: 18. 28114937 PMC5259972
  49. [50]Chen C., Wu M., Zhang W., Lu W., Zhang M., Zhang Z., Zhang X., Yuan Z. MicroRNA-939 restricts Hepatitis B virus by targeting Jmjd3-mediated and C/EBPalpha-coordinated chromatin remodeling. Sci. Rep. 2016; 6: 35974. 27779233 PMC5078794
  50. [51]Guo Z., Shao L., Zheng L., Du Q., Li P., John B., Geller D.A. miRNA-939 regulates human inducible nitric oxide synthase posttranscriptional gene expression in human hepatocytes. Proc. Natl. Acad. Sci. U.S.A. 2012; 109: 5826– 5831. 22451906 PMC3326458
  51. [52]Yang F., Nam S., Brown C.E., Zhao R., Starr R., Ma Y., Xie J., Horne D.A., Malkas L.H., Jove R. et al. A novel berbamine derivative inhibits cell viability and induces apoptosis in cancer stem-like cells of human glioblastoma, via up-regulation of miRNA-4284 and JNK/AP-1 signaling. PLoS One. 2014; 9: e94443. 24732116 PMC3986211
  52. [53]Li Y., Shen Z., Jiang H., Lai Z., Wang Z., Jiang K., Ye Y., Wang S. MicroRNA4284 promotes gastric cancer tumorigenicity by targeting ten-eleven translocation 1. Mol. Med. Rep. 2018; 17: 6569– 6575. 29512746 PMC5928641
  53. [54]Kim Y.K., Kim B., Kim V.N. Re-evaluation of the roles of DROSHA, Export in 5, and DICER in microRNA biogenesis. Proc. Natl. Acad. Sci. U.S.A. 2016; 113: E1881– E1889. 26976605 PMC4822641

Cited by

Sorted by citations

Authors
Alles, J., Fehlmann, T., Fischer, U., Backes, C., Galata, V., Minet, M., Hart, M., Abu-Halima, M., Grässer, F. A., Lenhof, H.-P., Keller, A., & Meese, E.
Affiliations
  • Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
  • Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
  • Institute of Virology, Saarland University Medical School, 66421 Homburg, Germany
  • Chair for Bioinformatics, Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
Venue
Nucleic Acids Research
Published
2019-03-01
Volume
47
Issue
7
Pages
3353-3364
ISSN
  • 0305-1048
  • 1362-4962
Cited by
555
References
1
Language
en
Funders
Michael J. Fox Foundation (14446)

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