Cluster analysis of regulatory sequences with a log likelihood ratio statistics-based similarity measure

Huiru Zheng, Haiying Wang, Jinglu Hu

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

Abstract

Upstream regions in the DNA sequence are characterized by the presence of short regulatory motifs, which function as target binding sites for transcription factors. Finding two genes with common motifs in their regulatory regions may aid users in identifying co-regulated genes or inferring regulatory modules. By modelling pattern occurrences in the regulatory regions with Poisson statistics, this paper presents a log likelihood ratio statistics-based distance measure to calculate pair-wise similarities between sequences. To perform cluster analysis of regulatory sequences, this paper introduces two clustering algorithms on the basis of the incorporation of the log likelihood ratio statistics-based distance into hierarchical clustering and Self-Organizing Map. The proposed approach has been tested on a synthetic dataset and a real biological example. The results indicate that, in comparison to traditional distance functions, the log likelihood ratio statistics-based similarity measure offers considerable improvements in the process of regulatory sequence-based gene classification.

Original languageEnglish
Title of host publicationProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Pages1220-1224
Number of pages5
DOIs
Publication statusPublished - 2007 Dec 1
Event7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE - Boston, MA, United States
Duration: 2007 Jan 142007 Jan 17

Publication series

NameProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Conference

Conference7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
CountryUnited States
CityBoston, MA
Period07/1/1407/1/17

Keywords

  • Cluster analysis
  • Log likelihood ratlio
  • Poisson distribution
  • Regulatory sequence

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Bioengineering

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