Type of Document Master's Thesis Author Kaur, Dipendra Author's Email Address dkaur1@student.gsu.edu URN etd-04182008-093111 Title MAPPING AND FILLING METABOLIC PATHWAY HOLES Degree Master of Science Department Bioinformatics Advisory Committee
Advisor Name Title Dr. Alexander Zelikovsky Committee Chair Dr. Robert Harrison Committee Co-Chair Dr. Irene Weber Committee Member Keywords
- Dipendra Kaur Thesis
- Filling Metabolic Pathway Holes
- Network Mapping
Date of Defense 2008-02-15 Availability unrestricted Abstract The network-mapping tool integrated with protein database search can be used for filling pathway holes. A metabolic pathway under consideration (pattern) is mapped into a known metabolic pathway (text), to find pathway holes. Enzymes that do not show up in the pattern may be a hole in the pattern pathway or an indication of alternative pattern pathway. We present a data-mining framework for filling holes in the pattern metabolic pathway based on protein function, prosite scan and protein sequence homology. Using this framework we suggest several fillings found with the same EC notation, with group neighbors (enzymes with same EC number in first three positions, different in the fourth position), and instances where the function of an enzyme has been taken up by the left or right neighboring enzyme in the pathway. The percentile scores are better when closely related organisms are mapped as compared to mapping distantly related organisms.Files
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