Complexities of human promoter sequences

Zhao, Fangcui; Yang, Huijie; Wang, Bing–Hong

doi:10.1016/j.jtbi.2007.03.035

Cited by 13 publications

(7 citation statements)

References 29 publications

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“…This finding is consistent with our report on the asymmetric distribution of the self-similar exponents of the promoters [21]. Because two different definitions of complexity are used, we cannot expect the same value of the ratio D left = D right .…”

Section: Resultssupporting

confidence: 93%

“…By means of the nonlinear modeling method, one can find that some segments are much more predictable compared with other segments [20]. In one of our recent works, by using the concept of diffusion entropy, we find that all the putative promoter sequences behave as scaleinvariant [21]. And the self-similar exponents distribute asymmetrically -namely, they contain two branches obeying the same Gaussian forms with different widths.…”

Section: Introductionmentioning

confidence: 89%

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Complexities of human promoter sequences

Jiang

Yang

Wang

2009

Physica A: Statistical Mechanics and its Applications

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Section: Resultssupporting

confidence: 93%

Section: Introductionmentioning

confidence: 89%

Complexities of human promoter sequences

Jiang

Yang

Wang

2009

Physica A: Statistical Mechanics and its Applications

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“…It is the first tool yielding correct scalings in both the Gaussian and the Lévy statistics. For this reason, it is used to detect scale-invariance in diverse research fields [43] , such as solar activities [44] – [48] , spectra of complex networks [49] , physiological signals [50] – [54] , DNA sequences [55] , [56] , geographical phenomena [57] – [59] , and finance [51] , [60] .…”

Section: Methodsmentioning

confidence: 99%

Evaluation of Scaling Invariance Embedded in Short Time Series

et al. 2014

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Scaling invariance of time series has been making great contributions in diverse research fields. But how to evaluate scaling exponent from a real-world series is still an open problem. Finite length of time series may induce unacceptable fluctuation and bias to statistical quantities and consequent invalidation of currently used standard methods. In this paper a new concept called correlation-dependent balanced estimation of diffusion entropy is developed to evaluate scale-invariance in very short time series with length . Calculations with specified Hurst exponent values of show that by using the standard central moving average de-trending procedure this method can evaluate the scaling exponents for short time series with ignorable bias () and sharp confidential interval (standard deviation ). Considering the stride series from ten volunteers along an approximate oval path of a specified length, we observe that though the averages and deviations of scaling exponents are close, their evolutionary behaviors display rich patterns. It has potential use in analyzing physiological signals, detecting early warning signals, and so on. As an emphasis, the our core contribution is that by means of the proposed method one can estimate precisely shannon entropy from limited records.

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“…Vinga and Almeida [9] introduced Rènyi's quadratic entropy to evaluate the randomness of DNA sequences. Zhao F, Yang H and Wang B [10] investigated the complexity of human promoter sequences by a diffusion entropy. Bose and Chouhan [3] studied the superinformation of the DNA sequence.…”

Section: Introductionmentioning

confidence: 99%

A Generalized Topological Entropy for Analyzing the Complexity of DNA Sequences

et al. 2014

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Topological entropy is one of the most difficult entropies to be used to analyze the DNA sequences, due to the finite sample and high-dimensionality problems. In order to overcome these problems, a generalized topological entropy is introduced. The relationship between the topological entropy and the generalized topological entropy is compared, which shows the topological entropy is a special case of the generalized entropy. As an application the generalized topological entropy in introns, exons and promoter regions was computed, respectively. The results indicate that the entropy of introns is higher than that of exons, and the entropy of the exons is higher than that of the promoter regions for each chromosome, which suggest that DNA sequence of the promoter regions is more regular than the exons and introns.

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Complexities of human promoter sequences

Cited by 13 publications

References 29 publications

Complexities of human promoter sequences

Complexities of human promoter sequences

Evaluation of Scaling Invariance Embedded in Short Time Series

A Generalized Topological Entropy for Analyzing the Complexity of DNA Sequences

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