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Cited by 167

The RNA Atlas expands the catalog of human non-coding RNAs

Lorenzi, Lucia, Chiu, Hua-Sheng, Avila Cobos, Francisco, Gross, Stephen, Volders, Pieter-Jan, Cannoodt, Robrecht, Nuytens, Justine, Vanderheyden, Katrien +28 more·2021·Nature Biotechnology
DOI 10.1038/s41587-021-00936-1
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  • Too many 'novel miRNAs' lack clear miRNA features and have only served to further complicate the miRNA field.

    “Too many “novel miRNAs” lack clear miRNA features and have only served to further complicate the miRNA field [17, 35, 36].”

    From A curated human cellular microRNAome based on 196 primary cell types (2022) · cites this paper as [17]

  • Of 640 samples from the RNA-Atlas project, 608 nonimmune cells consistently clustered together irrespective of their class/cell type expression and were removed.

    “Further, of 640 samples from the RNA-Atlas project [17], 608 (the nonimmune cells) consistently clustered together irrespective of their class/cell type expression. These were also removed, resulting in 2,077 final samples from 196 cell types.”

    From A curated human cellular microRNAome based on 196 primary cell types (2022) · cites this paper as [17]

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  1. Regev, A. et al. The Human Cell Atlas. eLife 6, e27041 (2017).
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  12. Gleeson, J., Lane, T. A., Harrison, P. J., Haerty, W. & Clark, M. B. Nanopore direct RNA sequencing detects differential expression between human cell populations. Preprint at bioRxiv https://doi.org/10.1101/2020.08.02.232785 (2020). · DOI
  13. Leger, A. et al. RNA modifications detection by comparative nanopore direct RNA sequencing. Preprint at bioRxiv https://doi.org/10.1101/843136 (2019). · DOI
  14. Nicorici, D. et al. FusionCatcher-a tool for finding somatic fusion genes in paired-end RNA-sequencing data. Preprint at https://doi. org/10.1101/011650 (2014). · DOI
  15. Goovaerts, T. et al. A comprehensive overview of genomic imprinting in breast and its deregulation in cancer. Nat. Commun. 9, 4120 (2018).
  16. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
  17. Liao Y, Smyth GK, Shi W. FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics https://doi.org/10.1093/bioinformatics/btt656 (2014). · DOI · Paper page
  18. Bovolenta, L. A., Acencio, M. L. & Lemke, N. HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions. BMC Genomics 13, 405 (2012).
  19. Whitfield, T. W. et al. Functional analysis of transcription factor binding sites in human promoters. Genome Biol. 13, R50 (2012).
  20. Haeussler, M. et al. The UCSC Genome Browser database: 2019 update. Nucleic Acids Res. 47, D853-D858 (2019). Reprints and permissions information is available at www.nature.com/reprints.
  21. Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46, D260-D266 (2018). 100. Pachkov, M., Balwierz, P. J., Arnold, P., Ozonov, E. & Van Nimwegen, E. SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res. 41, D214-D220 (2013). 101. Smith, A. D., Sumazin, P., Xuan, Z. & Zhang, M. Q. DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc. Natl Acad. Sci. USA 103, 6275-6280 (2006). 102. Smith, A. D., Sumazin, P., Das, D. & Zhang, M. Q. Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics 21 (Suppl. 1), i403-i412 (2005). 103.
  22. Lury, D. A. & Fisher, R. A. Statistical methods for research workers. J. R. Stat. Soc. Ser. D Statistician https://doi.org/10.2307/2986695 (1972). 106. Brown, M. B. 400: a method for combining non-independent, one-sided tests of significance. Biometrics 31, 987-992 (1975). 107. · DOI

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Authors
Lorenzi, L., Chiu, H.-S., Avila Cobos, F., Gross, S., Volders, P.-J., Cannoodt, R., Nuytens, J., Vanderheyden, K., Anckaert, J., Lefever, S., Tay, A. P., de Bony, E. J., Trypsteen, W., Gysens, F., Vromman, M., Goovaerts, T., Hansen, T. B., Kuersten, S., Nijs, N., Taghon, T., Vermaelen, K., Bracke, K. R., Saeys, Y., De Meyer, T., Deshpande, N. P., Anande, G., Chen, T.-W., Wilkins, M. R., Unnikrishnan, A., De Preter, K., Kjems, J., Koster, J., Schroth, G. P., Vandesompele, J., Sumazin, P., & Mestdagh, P.
ORCID
Venue
Nature Biotechnology
Publisher
Springer Science and Business Media LLC
Published
2021-06-17
Volume
39
Issue
11
Pages
1453-1465
ISSN
  • 1087-0156
  • 1546-1696
DOI
10.1038/s41587-021-00936-1
Cited by
167
References
14
Language
en
Update notices
correction (2021-06-28)
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