Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels

Fang Han Hsu, Erchin Serpedin, Yidong Chen, Edward R. Dougherty

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

DNA copy number alterations (CNAs) are known to be related to genetic diseases, including cancer. Our previous study proposed a stochastic model to investigate the relationship between copy number and gene expression values. The simulation results revealed that the relationship is not generally linear except when the ratio of transcription factor (TF) arrival rate to TF departure rate is large. However, only a transcription productive (ON) state was considered in the previous study. Under certain environmental conditions, the demand for mRNA is limited and hence the transcription is turned off and strictly regulated. In this study, an alternative (OFF) state of transcription is proposed, in which, bound TFs are assumed to be shut down, or unloaded, immediately after stimulating a transcription. Using the Laplace-Stieltjes transform and numerical analysis, the relationship between DNA copy number and gene expression level is evaluated. The stochastic models show that CNAs would potentially alter, or even reverse, the amplitude changes of gene expression levels between the productive (ON) state and the alternative (OFF) state.

Original languageEnglish
Title of host publicationProceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11
Pages83-86
Number of pages4
Publication statusPublished - 2011
Externally publishedYes
Event2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11 - San Antonio, TX, United States
Duration: 4 Dec 20116 Dec 2011

Other

Other2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11
CountryUnited States
CitySan Antonio, TX
Period4/12/116/12/11

Fingerprint

Transcription
Gene expression
Gene Expression
Transcription factors
Transcription Factors
Stochastic models
Inborn Genetic Diseases
DNA
Laplace transforms
Numerical analysis
Messenger RNA
Neoplasms

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computational Theory and Mathematics
  • Signal Processing
  • Biomedical Engineering

Cite this

Hsu, F. H., Serpedin, E., Chen, Y., & Dougherty, E. R. (2011). Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels. In Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11 (pp. 83-86). [6169449]

Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels. / Hsu, Fang Han; Serpedin, Erchin; Chen, Yidong; Dougherty, Edward R.

Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11. 2011. p. 83-86 6169449.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hsu, FH, Serpedin, E, Chen, Y & Dougherty, ER 2011, Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels. in Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11., 6169449, pp. 83-86, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11, San Antonio, TX, United States, 4/12/11.
Hsu FH, Serpedin E, Chen Y, Dougherty ER. Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels. In Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11. 2011. p. 83-86. 6169449
Hsu, Fang Han ; Serpedin, Erchin ; Chen, Yidong ; Dougherty, Edward R. / Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels. Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11. 2011. pp. 83-86
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