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Article: Improving the accuracy of signal transduction pathway construction using level-2 neighbours

TitleImproving the accuracy of signal transduction pathway construction using level-2 neighbours
Authors
KeywordsCell cycle pathway construction
Level-2 neighbours
MAPK pathway
MAPK pathway construction
Pathway construction
Protein pathway
Protein pathway construction
Randomised algorithm
Signal transduction pathway
System biology
Issue Date2010
PublisherInderscience Publishers. The Journal's web site is located at http://www.inderscience.com/ijbra
Citation
International Journal Of Bioinformatics Research And Applications, 2010, v. 6 n. 6, p. 542-555 How to Cite?
AbstractIn this paper, we consider the problem of reconstructing a pathway for a given set of proteins based on available genomics and proteomics information such as gene expression data. In all previous approaches, the scoring function for a candidate pathway usually only depends on adjacent proteins in the pathway. We propose to also consider proteins that are of distance two in the pathway (we call them Level-2 neighbours). We derive a scoring function based on both adjacent proteins and Level-2 neighbours in the pathway and show that our scoring function can increase the accuracy of the predicted pathways through a set of experiments. The problem of computing the pathway with optimal score, in general, is NP-hard. We thus extend a randomised algorithm to make it work on our scoring function to compute the optimal pathway with high probability. © 2010 Inderscience Enterprises Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/140788
ISSN
2015 SCImago Journal Rankings: 0.231
References

 

DC FieldValueLanguage
dc.contributor.authorWong, TKFen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorYiu, SMen_HK
dc.contributor.authorWong, SCKen_HK
dc.date.accessioned2011-09-23T06:19:20Z-
dc.date.available2011-09-23T06:19:20Z-
dc.date.issued2010en_HK
dc.identifier.citationInternational Journal Of Bioinformatics Research And Applications, 2010, v. 6 n. 6, p. 542-555en_HK
dc.identifier.issn1744-5485en_HK
dc.identifier.urihttp://hdl.handle.net/10722/140788-
dc.description.abstractIn this paper, we consider the problem of reconstructing a pathway for a given set of proteins based on available genomics and proteomics information such as gene expression data. In all previous approaches, the scoring function for a candidate pathway usually only depends on adjacent proteins in the pathway. We propose to also consider proteins that are of distance two in the pathway (we call them Level-2 neighbours). We derive a scoring function based on both adjacent proteins and Level-2 neighbours in the pathway and show that our scoring function can increase the accuracy of the predicted pathways through a set of experiments. The problem of computing the pathway with optimal score, in general, is NP-hard. We thus extend a randomised algorithm to make it work on our scoring function to compute the optimal pathway with high probability. © 2010 Inderscience Enterprises Ltd.en_HK
dc.languageengen_US
dc.publisherInderscience Publishers. The Journal's web site is located at http://www.inderscience.com/ijbraen_HK
dc.relation.ispartofInternational Journal of Bioinformatics Research and Applicationsen_HK
dc.rightsInternational Journal of Bioinformatics Research and Applications. Copyright © Inderscience Publishers.en_US
dc.subjectCell cycle pathway constructionen_HK
dc.subjectLevel-2 neighboursen_HK
dc.subjectMAPK pathwayen_HK
dc.subjectMAPK pathway constructionen_HK
dc.subjectPathway constructionen_HK
dc.subjectProtein pathwayen_HK
dc.subjectProtein pathway constructionen_HK
dc.subjectRandomised algorithmen_HK
dc.subjectSignal transduction pathwayen_HK
dc.subjectSystem biologyen_HK
dc.subject.meshAlgorithms-
dc.subject.meshDatabases, Protein-
dc.subject.meshGenomics-
dc.subject.meshIntracellular Signaling Peptides and Proteins - chemistry - genetics - metabolism-
dc.subject.meshSignal Transduction-
dc.titleImproving the accuracy of signal transduction pathway construction using level-2 neighboursen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1744-5485&volume=6&issue=6&spage=542&epage=555&date=2010&atitle=Improving+the+accuracy+of+signal+transduction+pathway+construction+using+level-2+neighbours-
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1504/IJBRA.2010.038736en_HK
dc.identifier.pmid21354961-
dc.identifier.scopuseid_2-s2.0-79952144869en_HK
dc.identifier.hkuros192199en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79952144869&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume6en_HK
dc.identifier.issue6en_HK
dc.identifier.spage542en_HK
dc.identifier.epage555en_HK
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWong, TKF=25423289800en_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.scopusauthoridWong, SCK=35319323100en_HK

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