Gene ontology friendly biclustering of expression profiles

Jinze Liu, Wei Wang, Jiong Yang

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

38 Scopus citations

Abstract

The soundness of clustering in the analysis of gene expression profiles and gene function prediction is based on the hypothesis that genes with similar expression profiles may imply strong correlations with their functions in the biological activities. Gene Ontology (GO) has become a well accepted standard in organizing gene function categories. Different gene function categories in GO can have very sophisticated relationships, such as 'part of and 'overlapping'. Until now, no clustering algorithm can generate gene clusters within which the relationships can naturally reflect those of gene function categories in the GO hierarchy. The failure in resembling the relationships may reduce the confidence of clustering in gene function prediction. In this paper, we present a new clustering technique, Smart Hierarchical Tendency Preserving clustering (SHTP-clustering), based on a bicluster model, Tendency Preserving cluster (TP-Cluster). By directly incorporating Gene Ontology information into the clustering process, the SHTP-clustering algorithm yields a TP-cluster tree within which any subtree can be well mapped to a part of the GO hierarchy. Our experiments on yeast cell cycle data demonstrate that this method is efficient and effective in generating the biological relevant TP-Clusters.

Original languageEnglish
Title of host publicationProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Pages436-447
Number of pages12
DOIs
StatePublished - 2004
EventProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 - Stanford, CA, United States
Duration: Aug 16 2004Aug 19 2004

Publication series

NameProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Conference

ConferenceProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Country/TerritoryUnited States
CityStanford, CA
Period8/16/048/19/04

Bibliographical note

Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.

Keywords

  • Biclustering
  • Gene Ontology
  • Gene expression profiles
  • Tendency Preserving

ASJC Scopus subject areas

  • Engineering (all)

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