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Postgraduate Thesis: Finding phenotype related pathways via biological networks comparison
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TitleFinding phenotype related pathways via biological networks comparison
 
AuthorsXiang, Lu.
项路.
 
Issue Date2011
 
PublisherThe University of Hong Kong (Pokfulam, Hong Kong)
 
Abstract Why some species (or strains of a species) exhibit certain phenotypes (e.g. aerobic, anaerobic, pathogenic etc.) while the others do not is an important question to be answered. Apart from the conventional genomic study, studying the metabolism of the two groups of species may discover the corresponding pathways that are conserved in one group but not in the other. However, only a few tools provide functions to compare two groups of metabolic networks which are usually limited to the reaction level, not the pathway level. In this dissertation, a problem named DMP (Differentiating Metabolic Pathway) problem was formed. Given two groups of metabolic networks, it aims at finding conserved pathways exist in first group, but not the second group. The problem also captures the mutation in similar pathways and derives a measurement (p-value and e-score) for evaluating the significance of the pathways. An algorithm, DMPFinder, was developed to solve the DMP problem. Experimental results show that DMPFinder is able to identify pathways that are critical for the first group to exhibit a certain phenotype which is absent in the other group. Some of these pathways cannot be identified by other tools which only consider reaction level or do not take into account possible mutations among species.
 
AdvisorsYiu, SM
 
DegreeMaster of Philosophy
 
SubjectSystems biology.
Metabolism - Data processing.
Bioinformatics.
Phenotype.
 
Dept/ProgramComputer Science
 
DOIhttp://dx.doi.org/10.5353/th_b4715262
 
DC FieldValue
dc.contributor.advisorYiu, SM
 
dc.contributor.authorXiang, Lu.
 
dc.contributor.author项路.
 
dc.date.hkucongregation2012
 
dc.date.issued2011
 
dc.description.abstract Why some species (or strains of a species) exhibit certain phenotypes (e.g. aerobic, anaerobic, pathogenic etc.) while the others do not is an important question to be answered. Apart from the conventional genomic study, studying the metabolism of the two groups of species may discover the corresponding pathways that are conserved in one group but not in the other. However, only a few tools provide functions to compare two groups of metabolic networks which are usually limited to the reaction level, not the pathway level. In this dissertation, a problem named DMP (Differentiating Metabolic Pathway) problem was formed. Given two groups of metabolic networks, it aims at finding conserved pathways exist in first group, but not the second group. The problem also captures the mutation in similar pathways and derives a measurement (p-value and e-score) for evaluating the significance of the pathways. An algorithm, DMPFinder, was developed to solve the DMP problem. Experimental results show that DMPFinder is able to identify pathways that are critical for the first group to exhibit a certain phenotype which is absent in the other group. Some of these pathways cannot be identified by other tools which only consider reaction level or do not take into account possible mutations among species.
 
dc.description.naturepublished_or_final_version
 
dc.description.thesisdisciplineComputer Science
 
dc.description.thesislevelmaster's
 
dc.description.thesisnameMaster of Philosophy
 
dc.identifier.doihttp://dx.doi.org/10.5353/th_b4715262
 
dc.identifier.hkulb4715262
 
dc.languageeng
 
dc.publisherThe University of Hong Kong (Pokfulam, Hong Kong)
 
dc.relation.ispartofHKU Theses Online (HKUTO)
 
dc.rightsThe author retains all proprietary rights, (such as patent rights) and the right to use in future works.
 
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License
 
dc.source.urihttp://hub.hku.hk/bib/B4715262X
 
dc.subject.lcshSystems biology.
 
dc.subject.lcshMetabolism - Data processing.
 
dc.subject.lcshBioinformatics.
 
dc.subject.lcshPhenotype.
 
dc.titleFinding phenotype related pathways via biological networks comparison
 
dc.typePG_Thesis
 
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 Why some species (or strains of a species) exhibit certain phenotypes (e.g. aerobic, anaerobic, pathogenic etc.) while the others do not is an important question to be answered. Apart from the conventional genomic study, studying the metabolism of the two groups of species may discover the corresponding pathways that are conserved in one group but not in the other. However, only a few tools provide functions to compare two groups of metabolic networks which are usually limited to the reaction level, not the pathway level. 

In this dissertation, a problem named DMP (Differentiating Metabolic Pathway) problem was formed. Given two groups of metabolic networks, it aims at finding conserved pathways exist in first group, but not the second group. The problem also captures the mutation in similar pathways and derives a measurement (p-value and e-score) for evaluating the significance of the pathways. 

An algorithm, DMPFinder, was developed to solve the DMP problem. Experimental results show that DMPFinder is able to identify pathways that are critical for the first group to exhibit a certain phenotype which is absent in the other group. Some of these pathways cannot be identified by other tools which only consider reaction level or do not take into account possible mutations among species.</description.abstract>
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