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Chen Liang Thesis 07-02-18.approved.pdf (3.18 MB)

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Motif Selection Using Simulated Annealing Algorithm with Application to Identify Regulatory Elements

Chen, Liang
http://orcid.org/0000-0002-8743-9977
http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1531343206505855

Abstract Details

2018, Master of Science (MS), Ohio University, Computer Science (Engineering and Technology).
Modern research on gene regulation and disorder-related pathways utilize the tools such as microarray and RNA-Seq to analyze the changes in the expression levels of large sets of genes. In silico motif discovery was performed based on the gene expression profile data, which generated a large set of candidate motifs (usually hundreds or thousands of motifs). How to pick a set of biologically meaningful motifs from the candidate motif set is a challenging biological and computational problem. As a computational problem it can be modeled as motif selection problem (MSP). Building solutions for motif selection problem will give biologists direct help in finding transcription factors (TF) that are strongly related to specific pathways and gaining insights of the relationships between genes. This study implemented an algorithm based on simulated annealing (SA) optimization algorithm for the motif selection problem, and investigated the properties of the implemented algorithm with the real world datasets (ENCODE project data). The results of evaluation based on ENCODE datasets indicate that simulated annealing algorithm is good for solving motif selection problem. The performance of simulated annealing algorithm can be tuned based on some parameters to fit for special requirements. Future improvement may be achieved via extending algorithm model (adaptive simulated annealing) and applying high dimensional cost function.
Lonnie Welch (Advisor)
Frank Drews (Committee Member)
Razvan Bunescu (Committee Member)
106 p.
Computer Science; Genetics; Molecular Biology
regulatory element; transcription factor; motif; motif selection; MSP; ENCODE; simulated annealing

Recommended Citations

Citations

  • Chen, L. (2018). Motif Selection Using Simulated Annealing Algorithm with Application to Identify Regulatory Elements [Master's thesis, Ohio University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1531343206505855

    APA Style (7th edition)

  • Chen, Liang. Motif Selection Using Simulated Annealing Algorithm with Application to Identify Regulatory Elements. 2018. Ohio University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1531343206505855.

    MLA Style (8th edition)

  • Chen, Liang. "Motif Selection Using Simulated Annealing Algorithm with Application to Identify Regulatory Elements." Master's thesis, Ohio University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1531343206505855

    Chicago Manual of Style (17th edition)

ohiou1531343206505855
528
© 2018, all rights reserved.
This open access ETD is published by Ohio University and OhioLINK.