Title page for ETD etd-07272005-110351

Type of Document Master's Thesis
Author Srinivasan, Venkataraghavan
URN etd-07272005-110351
Title A Biclustering Approach to Combinatorial Transcription Control
Degree Master of Science
Department Computer Science
Advisory Committee
Advisor Name Title
Murali, T. M. Committee Chair
Tyler, Brett M. Committee Co-Chair
Laubenbacher, Reinhard C. Committee Member
Zhang, Liqing Committee Member
  • Biclustering
  • Combinatorial transcription control
  • Promoter analysis
  • Random sampling
Date of Defense 2005-07-06
Availability restricted
Combinatorial control of transcription is a well established phenomenon in the cell. Multiple transcription factors often bind to the same transcriptional control region of a gene and interact with each other to control the expression of the gene. It is thus necessary to consider the joint conservation of sequence pairs in order to identify combinations of binding sites to which the transcription factors bind. Conventional motif finding algorithms fail to address this issue. We propose a novel biclustering algorithm based on random sampling to identify candidate binding site combinations. We establish bounds on the various parameters to the algorithm and study the conditions under which the algorithm is guaranteed to identify candidate binding sites. We analyzed a yeast cell cycle gene expression data set using our algorithm and recovered certain novel combinations of binding sites, besides those already reported in the literature.

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