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Article: An efficient method of computing impact degrees for multiple reactions in metabolic networks with cycles

TitleAn efficient method of computing impact degrees for multiple reactions in metabolic networks with cycles
Authors
KeywordsBoolean networks
Impact degree
Metabolic networks
Robustness
Issue Date2011
PublisherInstitute of Electronics, Information and Communication Engineers. The Journal's web site is located at http://search.ieice.org/bin/index.php?category=D&lang=E&curr=1
Citation
IEICE Transactions On Information And Systems, 2011, v. E94-D n. 12, p. 2393-2399 How to Cite?
AbstractThe impact degree is a measure of the robustness of a metabolic network against deletion of single or multiple reaction(s). Although such a measure is useful for mining important enzymes/genes, it was defined only for networks without cycles. In this paper, we extend the impact degree for metabolic networks containing cycles and develop a simple algorithm to calculate the impact degree. Furthermore we improve this algorithm to reduce computation time for the impact degree by deletions of multiple reactions. We applied our method to the metabolic network of E. coli, that includes reference pathways, consisting of 3281 reaction nodes and 2444 compound nodes, downloaded from KEGG database, and calculate the distribution of the impact degree. The results of our computational experiments show that the improved algorithm is 18.4 times faster than the simple algorithm for deletion of reaction-pairs and 11.4 times faster for deletion of reaction-triplets. We also enumerate genes with high impact degrees for single and multiple reaction deletions. © 2011 The Institute of Electronics, Information and Communication Engineers.
Persistent Identifierhttp://hdl.handle.net/10722/146395
ISSN
2012 Impact Factor: 0.218
2015 SCImago Journal Rankings: 0.212
ISI Accession Number ID
Funding AgencyGrant Number
JSPS23700017
Funding Information:

The work was partially supported by JSPS KAKENHI 23700017.

References

 

DC FieldValueLanguage
dc.contributor.authorTamura, Ten_HK
dc.contributor.authorCong, Yen_HK
dc.contributor.authorAkutsu, Ten_HK
dc.contributor.authorChing, WKen_HK
dc.date.accessioned2012-04-24T07:51:25Z-
dc.date.available2012-04-24T07:51:25Z-
dc.date.issued2011en_HK
dc.identifier.citationIEICE Transactions On Information And Systems, 2011, v. E94-D n. 12, p. 2393-2399en_HK
dc.identifier.issn0916-8532en_HK
dc.identifier.urihttp://hdl.handle.net/10722/146395-
dc.description.abstractThe impact degree is a measure of the robustness of a metabolic network against deletion of single or multiple reaction(s). Although such a measure is useful for mining important enzymes/genes, it was defined only for networks without cycles. In this paper, we extend the impact degree for metabolic networks containing cycles and develop a simple algorithm to calculate the impact degree. Furthermore we improve this algorithm to reduce computation time for the impact degree by deletions of multiple reactions. We applied our method to the metabolic network of E. coli, that includes reference pathways, consisting of 3281 reaction nodes and 2444 compound nodes, downloaded from KEGG database, and calculate the distribution of the impact degree. The results of our computational experiments show that the improved algorithm is 18.4 times faster than the simple algorithm for deletion of reaction-pairs and 11.4 times faster for deletion of reaction-triplets. We also enumerate genes with high impact degrees for single and multiple reaction deletions. © 2011 The Institute of Electronics, Information and Communication Engineers.en_HK
dc.languageengen_US
dc.publisherInstitute of Electronics, Information and Communication Engineers. The Journal's web site is located at http://search.ieice.org/bin/index.php?category=D&lang=E&curr=1en_HK
dc.relation.ispartofIEICE Transactions on Information and Systemsen_HK
dc.rightsIEICE Transactions on Information and Systems. Copyright © Institute of Electronics, Information and Communication Engineers.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subjectBoolean networksen_HK
dc.subjectImpact degreeen_HK
dc.subjectMetabolic networksen_HK
dc.subjectRobustnessen_HK
dc.titleAn efficient method of computing impact degrees for multiple reactions in metabolic networks with cyclesen_HK
dc.typeArticleen_HK
dc.identifier.emailChing, WK:wching@hku.hken_HK
dc.identifier.authorityChing, WK=rp00679en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1587/transinf.E94.D.2393en_HK
dc.identifier.scopuseid_2-s2.0-82655179239en_HK
dc.identifier.hkuros199183en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-82655179239&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volumeE94-Den_HK
dc.identifier.issue12en_HK
dc.identifier.spage2393en_HK
dc.identifier.epage2399en_HK
dc.identifier.isiWOS:000298304900013-
dc.publisher.placeJapanen_HK
dc.identifier.scopusauthoridTamura, T=13609056800en_HK
dc.identifier.scopusauthoridCong, Y=35185897700en_HK
dc.identifier.scopusauthoridAkutsu, T=7102080520en_HK
dc.identifier.scopusauthoridChing, WK=13310265500en_HK

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