Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

Inflated performance measures in enhancer–promoter interaction-prediction methods

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: The performance of using occurrences of real and shuffled motifs in window regions to predict enhancer–promoter interactions by using TargetFinder datasets.
Fig. 2: Analyses of TargetFinder and JEME.

Data availability

All data used in the manuscript are available at https://github.com/caofan/correspondence/.

Code availability

All code used in the manuscript are available at https://github.com/caofan/correspondence/.

References

  1. Lieberman-Aiden, E. et al. Science 326, 289–293 (2009).

    Article  CAS  Google Scholar 

  2. Fullwood, M. J. & Ruan, Y. J. Cell. Biochem. 107, 30–39 (2009).

    Article  CAS  Google Scholar 

  3. Whalen, S., Truty, R. M. & Pollard, K. S. Nat. Genet. 48, 488–496 (2016).

    Article  CAS  Google Scholar 

  4. Alipanahi, B., Delong, A., Weirauch, M. T. & Frey, B. J. Nat. Biotechnol. 33, 831–838 (2015).

    Article  CAS  Google Scholar 

  5. Quang, D. & Xie, X. Nucleic Acids Res. 44, e107 (2016).

    Article  Google Scholar 

  6. Wang, J. et al. Genome Res. 22, 1798–1812 (2012).

    Article  CAS  Google Scholar 

  7. Mathelier, A. et al. Nucleic Acids Res. 42, D142–D147 (2014).

    Article  CAS  Google Scholar 

  8. Yang, Y., Zhang, R., Singh, S. & Ma, J. Bioinformatics 33, i252–i260 (2017).

    Article  CAS  Google Scholar 

  9. Singh, S., Yang, Y., Poczos, B. & Ma, J. Quant. Biol. https://doi.org/10.1007/s40484-019-0154-0 (2019).

    Article  CAS  Google Scholar 

  10. Cao, Q. et al. Nat. Genet. 49, 1428–1436 (2017).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We would like to thank Q. Cao and Y.-L. Yip for providing us with JEME and TargetFinder’s training data on JEME’s random targets datasets and JEME’s training data on RIPPLE 5C datasets. We would like to thank all members of the laboratory of M.J.F. for helpful comments. This research was supported by the National Research Foundation (NRF) Singapore through an NRF Fellowship awarded to M.J.F. (NRF-NRFF2012-054) and Yale-NUS start-up funds awarded to M.J.F. This research was supported by the RNA Biology Center at the Cancer Science Institute of Singapore, NUS, as part of funding under the Singapore Ministry of Education Academic Research Fund Tier 3 awarded to D. G. Tenen (MOE2014-T3-1-006). This research is supported by the National Research Foundation Singapore and the Singapore Ministry of Education under its Research Centres of Excellence initiative.

Author information

Authors and Affiliations

Authors

Contributions

F.C. and M.J.F. conceived the research. F.C. performed the analyses. F.C. and M.J.F. reviewed the data and wrote the manuscript. All authors reviewed and approved of the manuscript.

Corresponding author

Correspondence to Melissa J. Fullwood.

Ethics declarations

Competing interests

The authors declare no competing interests.

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cao, F., Fullwood, M.J. Inflated performance measures in enhancer–promoter interaction-prediction methods. Nat Genet 51, 1196–1198 (2019). https://doi.org/10.1038/s41588-019-0434-7

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41588-019-0434-7

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing