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dc.contributor.authorCui, Jike
dc.contributor.authorDeLuca, Todd
dc.contributor.authorJung, Jae-Yoon
dc.contributor.authorWall, Dennis Paul Paul
dc.date.accessioned2013-03-19T16:31:06Z
dc.date.issued2011
dc.identifier.citationCui, Jike, Todd F DeLuca, Jae-Yoon Jung, and Dennis P Wall. 2011. Phylogenetically informed logic relationships improve detection of biological network organization. BMC Bioinformatics 12: 476.en_US
dc.identifier.issn1471-2105en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:10445588
dc.description.abstractBackground: A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite this success, few studies have attempted to search beyond just pairwise relationships among genes. Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses. Results: Taking advantage of a phylogenetic matrix constructed from the large orthologs database Roundup, we invented a method to create balanced profiles for individual triplets of genes that guarantee equal weight on the different phylogenetic scenarios of coevolution between genes. When we applied this idea to LAPP, the method to search for logic triplets of genes, the balanced profiles resulted in significant performance improvement and the discovery of hundreds of thousands more putative triplets than unadjusted profiles. We found that logic triplets detected biological network organization and identified key proteins and their functions, ranging from neighbouring proteins in local pathways, to well separated proteins in the whole pathway, and to the interactions among different pathways at the system level. Finally, our case study suggested that the directionality in a logic relationship and the profile of a triplet could disclose the connectivity between the triplet and surrounding networks. Conclusion: Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction.en_US
dc.language.isoen_USen_US
dc.publisherBioMed Centralen_US
dc.relation.isversionofdoi:10.1186/1471-2105-12-476en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402364/pdf/en_US
dash.licenseLAA
dc.titlePhylogenetically informed logic relationships improve detection of biological network organizationen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalBMC Bioinformaticsen_US
dash.depositing.authorWall, Dennis Paul Paul
dc.date.available2013-03-19T16:31:06Z
dc.identifier.doi10.1186/1471-2105-12-476*
dash.contributor.affiliatedDeLuca, Todd
dash.contributor.affiliatedJung, Jae-Yoon
dash.contributor.affiliatedWall, Dennis Paul


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