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Date of Award


Document Type

Campus Access Master's Report

Degree Name

Master of Science in Computer Science (MS)

Administrative Home Department

Department of Computer Science

Advisor 1

Hairong Wei

Committee Member 1

Laura Brown

Committee Member 2

Robert Pastel


Web applications of two algorithms, Top-down graphic Gaussian model (GGM) algorithm and Bottom-up GGM algorithm, for constructing multilayered hierarchical gene regulatory networks (ML-hGRNs) were implemented. Top-down GGM Algorithm is used for building a ML-hGRN mediated by a transcription factor (TF) while Bottom-up GGM Algorithm is for constructing a ML-hGRN operating above a biological pathway. In addition, a function for plotting ML-hGRN was developed. Moreover, two mathematical methods for TF reduction were implemented. One is sparse partial least square (SPLS) for identifying a pathway associated candidate regulatory genes, which can be used as inputs for the Bottom-up GGM Algorithm; the other is an algorithm for identifying TF-responsive genes from differentially expressed genes (DEGs). These TF-responsive genes can be used as inputs for the Top-down GGM Algorithm. The web applications I developed will be instrumental for biologists to identify hierarchical regulators through construction of ML-hGRNs.