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A Thesis Submitted in Partial Fulfillment of the Requirement for the Degree of Master of Science in Electrical Engineering

Mohammadi, Mahsa | 2016

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 48310 (05)
  4. University: Sharif University of Technology
  5. Department: Electrical Engieering
  6. Advisor(s): Jahed, Mehran; Motahhari, Abolfazl
  7. Abstract:
  8. Dnase I Hypersensitive Sites (DHSs) are known as comprehensive markers of DNA regulatory elements. The main function of regulatory elements is repressing or enhancing transcription of genes. Hence, the recruitment of the data is prevalent in many studies of genome. One of the applications of this data is to utilize it to predict active regulatory regions (Transcription Factor Binding Sites).There are different means to do this, divided in three major groups: first, the methods only use the number of DNase-seq reads that surround a candidate binding site. While robust, these methods do not reflect the shape of the signal. A second strategy uses a variety of approaches to model and identify the shape of the signal. A third method integrates DNase signal strength and shape with other features and data.The methods that use the shape of the signal can be utilized to analysis and model the shape of the signal. Here we first use a method based on the shape of the signal and then recruit some suggestions to improve the model and the results of the prediction. This is specifically viable when the resolution of the signal is weak. In this way one can discuss the probability of binding a specific transcription factor to a specific location, i.e. to check if some decease exists, with fewer experiments, but comparable results with more
  9. Keywords:
  10. Prediction ; DNA ; Trascription Factor Binding Sites (TFBS) ; Dnase I Hypersensitive Sites (DHSs) ; Regulatory Elements

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