Elucidation of Cysteine Richness in Arabidopsis Thaliana Genome Using Exact Distribution of Clump Statistics

Undergraduate #296
Discipline: Mathematics and Statistics
Subcategory:

Dustin Ford - Philander Smith College
Co-Author(s): Jocelyn Moore and Deidra Coleman, Philander Smith College, Little Rock, AR

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Arabidopsis thaliana is a model plant with a fully sequenced genome, small size and rapid growth rate. A. thaliana and other plants are immobile leaving them vulnerable to a multitude of predators, such as fungi, insects, bacteria, and animals. Plants have to rely on innate defense mechanisms in the forms of peptides and proteins, for example defensins, proteins rich in cysteine and disulfide bridges. A potential mathematical measure of cysteine richness emerged from recent methodology used to establish the over-abundance of a motif in a sequence. This measure specifically is the number of clumps of the motif. In this work, the observed number of clumps of cysteine within A. thaliana is obtained, and then the probability of outcomes or more extreme outcomes are obtain using the algorithm to compute the distribution of the number of clumps. With this, we conclude the statistical significance of the observed number of clumps through performing appropriate hypothesis testing and consequently establishing cysteine richness. In future work, cysteine richness will be confirmed using an alternative measure, namely coverage of the number of clumps, which has also proven to be a useful measure of over-abundance.

Funder Acknowledgement(s): NSF-EPSCOR grant DMS-1148695.

Faculty Advisor: Jocelyn Moore, jamoore@philander.edu

Role: All parts of this research was done by me.