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Refinement of Subnetwork Discovery Algorithm for Biological Networks

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abstract
The abundance of biological experimental data from new high-throughput technologies, such as microarray data, suggests the need for new methods to study biological processes using a systems-based approach. Handling this huge volume of data requires the development of new computational methods to analyze and extract interesting pieces of biological information. JAM (jActiveModules) is a Cytoscape plugin developed to nd connected sets of genes with high levels of di erential expression. This network approach helps biologists to generate new hypotheses concerning the biological mechanisms underlying observed changes in gene expression. In this work, the search algorithm of JAM is modi ed and measured. The goal was to improve the sensitivity and speci city of the method compared to the original JAM algorithm. The modi cations made to the search algorithm involve: randomizing the starting point of the search, constraining the number of subnetworks maintained while searching, and improving the regional-scoring heuristic. Importantly, these modi cations increase the number of signi cant genes observed in the results. To ensure consistency in the search results, we apply the search algorithm multiple times and develop a statistical lter to retain consistent genes appearing across JAM runs. Furthermore, we apply this improved version of JAM to DC (Dendritic Cell) maturation microarray data and KEGG pathways to study the underlying mechanisms behind the DC maturation process, an essential part of the development of protective immunity to a number of infectious pathogens.
subject
Computer Science
Computational Biology
contributor
Sajuthi, Satria (author)
Fetrow, Jacquelyn S. (committee chair)
Turkett, William H. (committee member)
Pauca, Victor Paul (committee member)
date
2010-05-07T20:21:58Z (accessioned)
2010-06-18T18:59:44Z (accessioned)
2010-05-07T20:21:58Z (available)
2010-06-18T18:59:44Z (available)
2010-05-07T20:21:58Z (issued)
degree
Computer Science (discipline)
identifier
http://hdl.handle.net/10339/14884 (uri)
language
en_US (iso)
publisher
Wake Forest University
rights
Release the entire work for access only to the Wake Forest University system for one year from the date below. After one year, release the entire work for access worldwide. (accessRights)
title
Refinement of Subnetwork Discovery Algorithm for Biological Networks
type
Thesis

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