Gene teams with relaxed proximity constraint

Sun Kim, Jeong-Hyeon Choi, Jiong Yang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

23 Citations (Scopus)

Abstract

Functionally related genes co-evolve, probably due to the strong selection pressure in evolution. Thus we expect that they are present in multiple genomes. Physical proximity among genes, known as gene team, is a very useful concept to discover functionally related genes in multiple genomes. However, there are also many gene sets that do not preserve physical proximity. In this paper, we generalized the gene team model, that looks for gene clusters in a physically clustered form, to multiple genome cases with relaxed constraint. We propose a novel hybrid pattern model that combines the set and the sequential pattern models. Our model searches for gene clusters with and/or without physical proximity constraint. This model is implemented and tested with 97 genomes (120 replicons). The result was analyzed to show the usefulness of our model. Especially, analysis of gene clusters that belong to B. subtilis and E. coli demonstrated that our model predicted many experimentally verified operons and functionally related clusters. Our program is fast enough to provide a sevice on the web at http://platcom.informatics.indiana.edu/platcom/. Users can select any combination of 97 genomes to predict gene teams.

Original languageEnglish (US)
Title of host publicationProceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005
Pages44-55
Number of pages12
Volume2005
StatePublished - Dec 1 2005
Externally publishedYes
Event2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005 - Stanford, CA, United States
Duration: Aug 8 2005Aug 11 2005

Other

Other2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005
CountryUnited States
CityStanford, CA
Period8/8/058/11/05

Fingerprint

Genes
Genome
Multigene Family
Replicon
Informatics
Operon
Escherichia coli
Pressure

ASJC Scopus subject areas

  • Engineering(all)
  • Medicine(all)

Cite this

Kim, S., Choi, J-H., & Yang, J. (2005). Gene teams with relaxed proximity constraint. In Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005 (Vol. 2005, pp. 44-55). [1498005]

Gene teams with relaxed proximity constraint. / Kim, Sun; Choi, Jeong-Hyeon; Yang, Jiong.

Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005. Vol. 2005 2005. p. 44-55 1498005.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Kim, S, Choi, J-H & Yang, J 2005, Gene teams with relaxed proximity constraint. in Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005. vol. 2005, 1498005, pp. 44-55, 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005, Stanford, CA, United States, 8/8/05.
Kim S, Choi J-H, Yang J. Gene teams with relaxed proximity constraint. In Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005. Vol. 2005. 2005. p. 44-55. 1498005
Kim, Sun ; Choi, Jeong-Hyeon ; Yang, Jiong. / Gene teams with relaxed proximity constraint. Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005. Vol. 2005 2005. pp. 44-55
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