Discovery of a Strongly-Interrelated Gene Network in Corals under Constant Darkness by Correlation Analysis after Wavelet Transform on Complex Network Model

<div><p>Coral reefs occupy a relatively small portion of sea area, yet serve as a crucial source of biodiversity by establishing harmonious ecosystems with marine plants and animals. Previous researches mainly focused on screening several key genes induced by stress. Here we proposed a novel method—correlation analysis after wavelet transform of complex network model, to explore the effect of light on gene expression in the coral <i>Acropora millepora</i> based on microarray data. In this method, wavelet transform and the conception of complex network were adopted, and 50 key genes with large differences were finally captured, including both annotated genes and novel genes without accurate annotation. These results shed light on our understanding of coral's response toward light changes and the genome-wide interaction among genes under the control of biorhythm, and hence help us to better protect the coral reef ecosystems. Further studies are needed to explore how functional connections are related to structural connections, and how connectivity arises from the interactions within and between different systems. The method introduced in this study for analyzing microarray data will allow researchers to explore genome-wide interaction network with their own dataset and understand the relevant biological processes.</p></div

Scatter diagrams of the Euclidean distances of the probes' expression data between the 2 groups.

<p>Scatter diagrams of the Euclidean distances of the probes' expression data between the 2 groups.</p

Annotated differentially-expressed probes with positive difference.

<p>Annotated differentially-expressed probes with positive difference.</p

Annotated differentially-expressed probes with negative difference.

<p>Annotated differentially-expressed probes with negative difference.</p

Difference of connectivity between LD group and DD group.

<p>A: Negative difference obtained by subtracting degree numbers of probes in DD group from degree numbers of corresponding probes in LD group. B: Positive difference gained throughout subtracting degree numbers of probes in DD group from degree numbers of corresponding probes in LD group. C: Negative difference curve by smoothing scatter diagram of negative difference in A. D: Positive difference curve by smoothing scatter diagram of positive difference in B.</p