Abstract
In this work, a novel method was developed to distinguish nucleosome DNA and linker DNA based on increment of diversity combined with quadratic discriminant analysis (IDQD), using k-mer frequency of nucleotides in genome. When used to predict DNA potential for forming nucleosomes, the model achieved a high accuracy of 94.94%, 77.60%, and 86.81%, respectively, for Saccharomyces cerevisiae, Homo sapiens, and Drosophila melanogaster. The area under the receiver operator characteristics curve of our classifier was 0.982 for S. cerevisiae. Our results indicate that DNA sequence preference is critical for nucleosome formation potential and is likely conserved across eukaryotes. The model successfully identified nucleosome-enriched or nucleosome-depleted regions in S. cerevisiae genome, suggesting nucleosome positioning depends on DNA sequence preference. Thus, IDQD classifier is useful for predicting nucleosome positioning.
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Abbreviations
- IDQD:
-
Increment of diversity combined with quadratic discriminant analysis
- CHIP-chip:
-
Chromatin immunoprecipitation coupled with microarrays
- CHIP-Seq:
-
Chromatin immunoprecipitation coupled with sequencing techniques
- ROC:
-
Receiver operator characteristics
- auROC:
-
The area under the ROC curve
- MCC:
-
Matthew’s correlation coefficient
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Acknowledgments
We are very grateful to J.Y. Wang for the helpful suggestion. This research was supported by Natural Science Foundation of China (Grant No. 60761001, 61072129).
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Zhao, X., Pei, Z., Liu, J. et al. Prediction of nucleosome DNA formation potential and nucleosome positioning using increment of diversity combined with quadratic discriminant analysis. Chromosome Res 18, 777–785 (2010). https://doi.org/10.1007/s10577-010-9160-9
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DOI: https://doi.org/10.1007/s10577-010-9160-9