Mining time-shifting co-regulation patterns from gene expression data

G. Yin*, Yuhai Zhao, Bin Zhang, Guoren Wang

*Corresponding author for this work

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

11 Citations (Scopus)

Abstract

Previous work for finding patterns only focuses on grouping objects under the same subset of dimensions. Thus, an important bio-interesting pattern, i.e. time-shifting, will be ignored during the analysis of time series gene expression data. In this paper, we propose a new definition of coherent cluster for time series gene expression data called ts-cluster. The proposed model allows (1) the expression profiles of genes in a cluster to be coherent on different subsets of dimensions, i.e. these genes follow a certain time-shifting relationship, and (2) relative expression magnitude is taken into consideration instead of absolute one, which can tolerate the negative impact induced by "noise". This work is missed by previous research, which facilitates the study of regulatory relationships between genes. A novel algorithm is also presented and implemented to mine all the significant ts-clusters. Results experimented on both synthetic and real datasets show the ts-cluster algorithm is able to efficiently detect a significant amount of clusters missed by previous model, and these clusters are potentially of high biological significance.

Original languageEnglish
Title of host publicationAdvances in Data and Web Management - Joint 9th Asia-Pacific Web Conference, APWeb 2007 and 8th International Conference on Web-Age Information Management, WAIM 2007, Proceedings
PublisherSpringer Verlag
Pages62-73
Number of pages12
ISBN (Print)9783540724834
DOIs
Publication statusPublished - 2007
Externally publishedYes
EventJoint 9th Asia-Pacific Web Conference on Advances in Data and Web Management, APWeb 2007 and 8th International Conference on Web-Age Information Management, WAIM 2007 - Huang Shan, China
Duration: 16 Jun 200718 Jun 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4505 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

ConferenceJoint 9th Asia-Pacific Web Conference on Advances in Data and Web Management, APWeb 2007 and 8th International Conference on Web-Age Information Management, WAIM 2007
Country/TerritoryChina
CityHuang Shan
Period16/06/0718/06/07

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