Off-campus Michigan Tech users: To download campus access theses or dissertations, please use the following button to log in with your Michigan Tech ID and password: log in to proxy server
Non-Michigan Tech users: Please talk to your librarian about requesting this thesis or dissertation through interlibrary loan.
Title
Systemic analysis of microarray data sets towards identifying genes regulating root development
Date of Award
2011
Document Type
Master's report
Degree Name
Master of Science in Computer Science (MS)
College, School or Department Name
Department of Computer Science
First Advisor
Hairong Wei
Abstract
Nitrogen and water are essential for plant growth and development. In this study, we designed experiments to produce gene expression data of poplar roots under nitrogen starvation and water deprivation conditions. We found low concentration of nitrogen led first to increased root elongation followed by lateral root proliferation and eventually increased root biomass. To identify genes regulating root growth and development under nitrogen starvation and water deprivation, we designed a series of data analysis procedures, through which, we have successfully identified biologically important genes. Differentially Expressed Genes (DEGs) analysis identified the genes that are differentially expressed under nitrogen starvation or drought. Protein domain enrichment analysis identified enriched themes (in same domains) that are highly interactive during the treatment. Gene Ontology (GO) enrichment analysis allowed us to identify biological process changed during nitrogen starvation. Based on the above analyses, we examined the local Gene Regulatory Network (GRN) and identified a number of transcription factors. After testing, one of them is a high hierarchically ranked transcription factor that affects root growth under nitrogen starvation.
It is very tedious and time-consuming to analyze gene expression data. To avoid doing analysis manually, we attempt to automate a computational pipeline that now can be used for identification of DEGs and protein domain analysis in a single run. It is implemented in scripts of Perl and R.
Recommended Citation
Zhang, Hang, "Systemic analysis of microarray data sets towards identifying genes regulating root development", Master's report, Michigan Technological University, 2011.