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dc.contributor.authorWong, Ka Chun
dc.contributor.authorPeng, Chengbin
dc.contributor.authorWong, Manhon
dc.contributor.authorLeung, Kwongsak
dc.date.accessioned2015-08-03T09:02:55Z
dc.date.available2015-08-03T09:02:55Z
dc.date.issued2011-02-05
dc.identifier.issn14327643
dc.identifier.doi10.1007/s00500-011-0692-5
dc.identifier.urihttp://hdl.handle.net/10754/561713
dc.description.abstractProtein-DNA bindings are essential activities. Understanding them forms the basis for further deciphering of biological and genetic systems. In particular, the protein-DNA bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) play a central role in gene transcription. Comprehensive TF-TFBS binding sequence pairs have been found in a recent study. However, they are in one-to-one mappings which cannot fully reflect the many-to-many mappings within the bindings. An evolutionary algorithm is proposed to learn generalized representations (many-to-many mappings) from the TF-TFBS binding sequence pairs (one-to-one mappings). The generalized pairs are shown to be more meaningful than the original TF-TFBS binding sequence pairs. Some representative examples have been analyzed in this study. In particular, it shows that the TF-TFBS binding sequence pairs are not presumably in one-to-one mappings. They can also exhibit many-to-many mappings. The proposed method can help us extract such many-to-many information from the one-to-one TF-TFBS binding sequence pairs found in the previous study, providing further knowledge in understanding the bindings between TFs and TFBSs. © 2011 Springer-Verlag.
dc.description.sponsorshipThe authors are grateful to the anonymous reviewers for their valuable comments. They would like to thank Tak-Ming Chan for his help on surveying the related works. This research is partially supported by the grants from the Research Grants Council of the Hong Kong Special Administrative Region, China (Project Nos. 414107 and 414708).
dc.publisherSpringer Nature
dc.subjectBioinformatics
dc.subjectCrowding
dc.subjectDNA
dc.subjectGene transcription
dc.subjectPDB
dc.subjectProtein
dc.subjectSequence
dc.subjectTRANSFAC
dc.titleGeneralizing and learning protein-DNA binding sequence representations by an evolutionary algorithm
dc.typeArticle
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentComputer Science Program
dc.identifier.journalSoft Computing
dc.contributor.institutionDepartment of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
kaust.personPeng, Chengbin
kaust.personWong, Ka Chun
dc.date.published-online2011-02-05
dc.date.published-print2011-08


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