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A Ratiometric-Based Measure of Gene Co-Expression


Abelin, Anna Cecilia Therese (2014) A Ratiometric-Based Measure of Gene Co-Expression. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9JH3J5B.


Current measures of global gene expression analyses, such as correlation and mutual information-based approaches, largely depend on the degree of association between mRNA levels and to a lesser extent on variability. I develop and implement a new approach, called the Ratiometric method, which is based on the coefficient of variation of the expression ratio of two genes, relying more on variation than previous methods. The advantage of such modus operandi is the ability to detect possible gene pair interactions regardless of the degree of expression dispersion across the sample group. Gene pairs with low expression dispersion, i.e., their absolute expressions remain constant across the sample group, are systematically missed by correlation and mutual information analyses. The superiority of the Ratiometric method in finding these gene pair interactions is demonstrated in a data set of RNA-seq B-cell samples from the 1000 Genomes Project Consortium. The Ratiometric method renders a more comprehensive recovery of KEGG pathways and GO-terms.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Ratio, Ratiometric, gene expression analysis, transcriptome, fold-change
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Biology
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Wold, Barbara J.
Thesis Committee:
  • Sternberg, Paul W. (chair)
  • Wold, Barbara J.
  • Bronner, Marianne E.
  • Guttman, Mitchell
Defense Date:30 April 2014
Record Number:CaltechTHESIS:05072014-160838588
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8226
Deposited By: Anna Abelin
Deposited On:25 Nov 2014 23:08
Last Modified:08 Nov 2023 00:36

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