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Promoter prediction analysis on the whole human genome

Nature Biotechnology volume 22, pages 1467–1473 (2004)Cite this article

Abstract

Promoter prediction programs (PPPs) are important for in silico gene discovery without support from expressed sequence tag (EST)/cDNA/mRNA sequences, in the analysis of gene regulation and in genome annotation. Contrary to previous expectations, a comprehensive analysis of PPPs reveals that no program simultaneously achieves sensitivity and a positive predictive value >65%. PPP performances deduced from a limited number of chromosomes or smaller data sets do not hold when evaluated at the level of the whole genome, with serious inaccuracy of predictions for non-CpG-island-related promoters. Some PPPs even perform worse than, or close to, pure random guessing.

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Acknowledgements

We are grateful to Riu Yamashita and Kenta Nakai for assisting in constructing and maintaining DBTSS.

Author information

Authors and Affiliations

  1. Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613, Singapore

    Vladimir B Bajic & Sin Lam Tan

  2. Human Genome Center, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan

    Yutaka Suzuki & Sumio Sugano

Authors
  1. Vladimir B Bajic
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  2. Sin Lam Tan
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  3. Yutaka Suzuki
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  4. Sumio Sugano
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Corresponding author

Correspondence to Vladimir B Bajic.

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Competing interests

The employer of Vladimir B. Bajic and Sin Lam Tan has licensed Dragon Promoter Finder and Dragon Gene Start Finder to Biobase, Germany. Vladimir B. Bajic receives royalty for these two programs.

Supplementary information

Supplementary Figure 1

Distribution of clustered predictions for seven analyzed PPPs.

Supplementary Table 1

Results of promoter prediction on human chromosomes 21 and 22.

Supplementary Table 2

Results of promoter prediction on human chromosomes 4, 21 and 22.

Supplementary Table 3

Results of promoter prediction on HG for different distance criteria.

Supplementary Methods

Supplementary Notes

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Bajic, V., Tan, S., Suzuki, Y. et al. Promoter prediction analysis on the whole human genome. Nat Biotechnol 22, 1467–1473 (2004). https://doi.org/10.1038/nbt1032

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