Abstract/Details

Functional inference and pattern discovery from integrated Saccharomyces cerevisiae networks


2005 2005

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Abstract (summary)

My thesis focuses on functional inference and pattern discovery from integrated S. cerevisiae networks. The rapid advancement of genomic and proteomic research in the budding yeast has provided us, on a large scale, with information on various characteristics of genes or proteins as well as various types of interactions or relationships between genes or proteins. To represent all above information in a combined manner, we constructed an integrated S. cerevisiae network, in which nodes are genes or proteins, labeled with their characteristics, and links are interactions or relationships between genes or proteins, colored according to their relationship types.

Features of the integrated S. cerevisiae network can be utilized to make functional inferences. We first integrated multiple gene- or protein-pair characteristics using probabilistic decision trees and accurately predicted co-complexed relationship, which may represent functional association between proteins. Next, we demonstrated that direct function prediction can be made successfully by integrating both gene characteristics and various types of gene- or protein-pair relationships using a fully integrated probabilistic model.

The integrated S. cerevisiae network also exhibits recurring interconnection patterns such as network motifs. We explored an integrated S. cerevisiae network composed of five different link types and discovered multi-colored network motifs, as well as network themes—classes of higher-order recurring interconnection patterns that encompass multiple occurrences of network motifs. We also represented the integrated S. cerevisiae network in terms of network themes, which provides a useful simplification of the otherwise confusing tangle of biological relationships.

Indexing (details)


Subject
Molecular biology
Classification
0307: Molecular biology
Identifier / keyword
Biological sciences; Functional inference; Integrated networks; Protein-protein interactions
Title
Functional inference and pattern discovery from integrated Saccharomyces cerevisiae networks
Author
Zhang, Lan
Number of pages
195
Publication year
2005
Degree date
2005
School code
0084
Source
DAI-B 66/05, Dissertation Abstracts International
Place of publication
Ann Arbor
Country of publication
United States
ISBN
9780542120343, 0542120348
Advisor
Roth, Frederick P.
University/institution
Harvard University
University location
United States -- Massachusetts
Degree
Ph.D.
Source type
Dissertations & Theses
Language
English
Document type
Dissertation/Thesis
Dissertation/thesis number
3174085
ProQuest document ID
305000730
Copyright
Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.
Document URL
http://search.proquest.com/docview/305000730
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