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Conference Paper: DMPFinder - Finding differentiating pathways with gaps from two groups of metabolic networks

TitleDMPFinder - Finding differentiating pathways with gaps from two groups of metabolic networks
Authors
Issue Date2011
Citation
The 3rd International Conference on Bioinformatics and Computational Biology (BICoB 2011), New Orleans, LA., 23-25 March 2011. How to Cite?
AbstractWhy some strains of a species exhibit a certain phenotype (e.g. drug resistant) but not the other strains of the same species is a critical question to answer. Studying the metabolism of the two groups of strains may discover the corresponding pathways that are conserved in the first group but not in the second group. 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 paper, we formulate the DMP (Differentiating Metabolic Pathway) problem for finding conserved pathways exist in first group, but not the second group. The problem also captures the mutation in pathways and derives a measure (p-value and e-score) for evaluating the confident of the pathways. We then developed an algorithm, DMPFinder, 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. The software is available at: http://i.cs.hku.hk/alse/hkubrg/projects/DMPFinder/
DescriptionSession 2B: Biological and Regulatory Networks
Persistent Identifierhttp://hdl.handle.net/10722/135708

 

DC FieldValueLanguage
dc.contributor.authorLeung, HCMen_US
dc.contributor.authorLeung, SYen_US
dc.contributor.authorXiang, CLen_US
dc.contributor.authorYiu, SMen_US
dc.contributor.authorChin, FYLen_US
dc.date.accessioned2011-07-27T01:47:03Z-
dc.date.available2011-07-27T01:47:03Z-
dc.date.issued2011en_US
dc.identifier.citationThe 3rd International Conference on Bioinformatics and Computational Biology (BICoB 2011), New Orleans, LA., 23-25 March 2011.en_US
dc.identifier.urihttp://hdl.handle.net/10722/135708-
dc.descriptionSession 2B: Biological and Regulatory Networks-
dc.description.abstractWhy some strains of a species exhibit a certain phenotype (e.g. drug resistant) but not the other strains of the same species is a critical question to answer. Studying the metabolism of the two groups of strains may discover the corresponding pathways that are conserved in the first group but not in the second group. 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 paper, we formulate the DMP (Differentiating Metabolic Pathway) problem for finding conserved pathways exist in first group, but not the second group. The problem also captures the mutation in pathways and derives a measure (p-value and e-score) for evaluating the confident of the pathways. We then developed an algorithm, DMPFinder, 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. The software is available at: http://i.cs.hku.hk/alse/hkubrg/projects/DMPFinder/-
dc.languageengen_US
dc.relation.ispartofInternational Conference on Bioinformatics and Computational Biologyen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleDMPFinder - Finding differentiating pathways with gaps from two groups of metabolic networksen_US
dc.typeConference_Paperen_US
dc.identifier.emailLeung, HCM: cmleung2@cs.hku.hken_US
dc.identifier.emailLeung, SY: syleung@cs.hku.hken_US
dc.identifier.emailXiang, CL: lxiang2@cs.hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hk-
dc.identifier.emailChin, FYL: chin@cs.hku.hk-
dc.identifier.authorityLeung, HCM=rp00144en_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.identifier.authorityChin, FYL=rp00105en_US
dc.description.naturepostprint-
dc.identifier.hkuros187811en_US
dc.description.otherThe 3rd International Conference on Bioinformatics and Computational Biology (BICoB 2011), New Orleans, LA., 23-25 March 2011.-

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