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Reply to ‘Inflated performance measures in enhancer–promoter interaction-prediction methods’

Nature Genetics volume 51, pages 1201–1202 (2019)Cite this article

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Cao and Yip reply — Cao and Fullwood1 argue that the reported performance of JEME2 was affected by the presence of positive pairs of enhancers and transcription start sites (TSSs) in the training and testing sets that overlap in their window regions. They also show that our random targets approach to generating negative pairs led to very different distance distributions for the positive and negative pairs (Fig. 2g in ref. 1), thus making it trivial to separate the positives and negatives on the basis of genomic distance features alone.

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Fig. 1: Relationship between enhancer–TSS genomic distance and JEME performance.

Data availability

The data that support the findings of this study are available at http://yiplab.cse.cuhk.edu.hk/jeme/.

References

  1. Cao, F. & Fullwood, M. J. Nat. Genet. https://doi.org/10.1038/s41588-019-0434-7 (2019).

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

    Article  CAS  Google Scholar 

  3. Roy, S. et al. Nucleic Acids Res. 43, 8694–8712 (2015).

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Authors and Affiliations

  1. School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong

    Qin Cao

  2. Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong

    Kevin Y. Yip

  3. Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong

    Kevin Y. Yip

  4. CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong

    Kevin Y. Yip

  5. Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong

    Kevin Y. Yip

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  1. Qin Cao
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  2. Kevin Y. Yip
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Contributions

Q.C. and K.Y.Y. designed the analyses. Q.C. carried out the analyses. Q.C. and K.Y.Y. interpreted the data and prepared the manuscript.

Corresponding author

Correspondence to Kevin Y. Yip.

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The authors declare no competing interests.

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Cao, Q., Yip, K.Y. Reply to ‘Inflated performance measures in enhancer–promoter interaction-prediction methods’. Nat Genet 51, 1201–1202 (2019). https://doi.org/10.1038/s41588-019-0452-5

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  • DOI: https://doi.org/10.1038/s41588-019-0452-5

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