Date of Graduation

12-2019

Document Type

Thesis

Degree Name

Master of Science in Statistics and Analytics (MS)

Degree Level

Graduate

Department

Mathematical Sciences

Advisor/Mentor

Qingyang Zhang

Committee Member

Giovanni Petris

Second Committee Member

Mark Arnold

Third Committee Member

Jyotishka Datta

Keywords

gene expression, gene regulatory network analysis, molecular signatures

Abstract

Background

Gene expression profiling by microarray has been used to uncover molecular variations in many different diseases. Complementary to conventional differential expression analysis, differential co-expression analysis can identify gene markers from the systematic and granular level. There are three aspects for differential co-expression network analysis, including the network global topological comparison, differential co-expression cluster identification, and differential co-expressed genes and gene pair identification. To date, most of the methods available still rely on Pearson’s correlation coefficient despite its nonlinear insensitivity.

Results

Here we present an approach that is robust to nonlinearity by using the edge-count test for differential co-expression analysis. The performance of the new approach was tested with synthetic data and found to have significant results. For real data, we used a human cervical cancer data set prepared from 29 pairs of cervical tumor and matched normal tissue samples. Hierarchical cluster analysis resulted in the identification of clusters containing differentially co-expressed genes associated with the regulation of cervical cancer.

Conclusion

The proposed approach targets all different types of differential co-expression and it is sensitive to nonlinear relations. It is easy to implement and can be applied to any sequencing data to identify gene co-expression differences between multiple conditions.

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