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Gravitropic Signal Transduction: A Systems Approach to Gene Discovery
Kaiyu Shen
Gravity is an important stimulus for plants. Gravitropism, the plants’ response to
gravity, can be divided into three phases: gravity perception, signal transduction and
response. Various theories have been proposed to explain the process of gravitropism,
yet more genes are needed to elucidate the mechanism of gravitropic signal transduction.
A transcriptome analysis, in combination with the Gravity Persistent Signal treatment,
was performed to specifically study the genes involved in signal transduction. A list of
differentially expressed genes was discovered, and five selected for further physiological
validation.
In addition to the standard analysis of differentially expressed genes, a
systematic approach was adopted to uncover more gravity related genes.
semi-supervised learning method was applied to find novel gravity genes.
A
This learning
method took a set of known gravity genes as well as a collection of heterogeneous
annotation features as input and generated a list of genes that are functionally related to
gravity signal transduction. Based on the list of gravity related genes, a potential
interaction network was predicted based two approaches: a dynamic Bayesian network
and a time-lagged correlation coefficient.
The intersection of these networks was
further investigated for hub and bottleneck genes.
Such an approach provides a
framework to extend current research in a more comprehensive manner.