Learning Gene Regulatory Networks Computationally from Gene Expression Data Using Weighted Consensus
Type
ThesisAuthors
Fujii, Chisato
Advisors
Gao, Xin
Committee members
Soloviev, VictorHoehndorf, Robert

Program
Computer ScienceDate
2015-04-16Embargo End Date
2016-04-16Permanent link to this record
http://hdl.handle.net/10754/550417
Metadata
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At the time of archiving, the student author of this thesis opted to temporarily restrict access to it. The full text of this thesis became available to the public after the expiration of the embargo on 2016-04-16.Abstract
Gene regulatory networks analyze the relationships between genes allowing us to un- derstand the gene regulatory interactions in systems biology. Gene expression data from the microarray experiments is used to obtain the gene regulatory networks. How- ever, the microarray data is discrete, noisy and non-linear which makes learning the networks a challenging problem and existing gene network inference methods do not give consistent results. Current state-of-the-art study uses the average-ranking-based consensus method to combine and average the ranked predictions from individual methods. However each individual method has an equal contribution to the consen- sus prediction. We have developed a linear programming-based consensus approach which uses learned weights from linear programming among individual methods such that the methods have di↵erent weights depending on their performance. Our result reveals that assigning di↵erent weights to individual methods rather than giving them equal weights improves the performance of the consensus. The linear programming- based consensus method is evaluated and it had the best performance on in silico and Saccharomyces cerevisiae networks, and the second best on the Escherichia coli network outperformed by Inferelator Pipeline method which gives inconsistent results across a wide range of microarray data sets.Citation
Fujii, C. (2015). Learning Gene Regulatory Networks Computationally from Gene Expression Data Using Weighted Consensus. KAUST Research Repository. https://doi.org/10.25781/KAUST-1A8VVae974a485f413a2113503eed53cd6c53
10.25781/KAUST-1A8VV