Decoupling Linear and Nonlinear Associations of Gene Expression

  • Alan Itakura

Student thesis: Master's Thesis

Abstract

The FANTOM consortium has generated a large gene expression dataset of different cell lines and tissue cultures using the single-molecule sequencing technology of HeliscopeCAGE. This provides a unique opportunity to investigate novel associations between gene expression over time and different cell types. Here, we create a MatLab wrapper for a powerful and computationally intensive set of statistics known as Maximal Information Coefficient, and then calculate this statistic for a large, comprehensive dataset containing gene expression of a variety of differentiating tissues. We then distinguish between linear and nonlinear associations, and then create gene association networks. Following this analysis, we are then able to identify clusters of linear gene associations that then associate nonlinearly with other clusters of linearity, providing insight to much more complex connections between gene expression patterns than previously anticipated.
Date of AwardMay 2013
Original languageEnglish (US)
Awarding Institution
  • Biological, Environmental Science and Engineering
SupervisorTimothy Ravasi (Supervisor)

Keywords

  • Nonlinear associations
  • Linear associations
  • FANTOM
  • Modularity

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