ArticleChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology2010
Prediction of nucleosome DNA formation potential and nucleosome positioning using increment of diversity combined with quadratic discriminant analysis.
Article in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 21 citations in OpenAlex.
- Short tandem repeats delineate gene bodies across eukaryotes.Nature communications · 2024Article
- Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences.BMC genomics · 2024Article
- Circ-LocNet: A Computational Framework for Circular RNA Sub-Cellular Localization Prediction.International journal of molecular sciences · 2022Article
- A deformation energy model reveals sequence-dependent property of nucleosome positioning.Chromosoma · 2021Article
- Predicting Bacteriophage Enzymes and Hydrolases by Using Combined Features.Frontiers in bioengineering and biotechnology · 2020Article
- Article
- Nucleosome Positioning with Set of Key Positions and Nucleosome Affinity.The open biomedical engineering journal · 2014Article
- Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2012Article
- Predicting nucleosome binding motif set and analyzing their distributions around functional sites of human genes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2012Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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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