Finding similar patterns in microarray data

Edited book (chapter)

Chen, Xiangsheng, Li, Jiuyong, Daggard, Grant and Huang, Xiaodi. 2005. "Finding similar patterns in microarray data." Zhang, Shichao and Jarvis, Ray (ed.) AI 2005: Advances in artificial intelligence. Berlin, Germany. Springer. pp. 1272-1276
Chapter Title

Finding similar patterns in microarray data

Book Chapter CategoryEdited book (chapter)
ERA Publisher ID3337
Book TitleAI 2005: Advances in artificial intelligence
AuthorsChen, Xiangsheng (Author), Li, Jiuyong (Author), Daggard, Grant (Author) and Huang, Xiaodi (Author)
EditorsZhang, Shichao and Jarvis, Ray
Page Range1272-1276
SeriesLecture Notes in Computer Science
Number of Pages5
Year2005
PublisherSpringer
Place of PublicationBerlin, Germany
ISBN3540304622
ISSN0302-9743
Digital Object Identifier (DOI)https://doi.org/10.1007/11589990_185
Web Address (URL)https://link.springer.com/chapter/10.1007/11589990_185
Abstract

In this paper we propose a clustering algorithm called s-Cluster for analysis of gene expression data based on pattern-similarity. The algorithm captures the tight clusters exhibiting strong similar expression patterns in Microarray data,and allows a high level of overlap among discovered clusters without completely grouping all genes like other algorithms. This reflects the biological fact that not all functions are turned on in an experiment, and that many genes are co-expressed in multiple groups in response to different stimuli. The experiments have demonstrated that the proposed algorithm successfully groups the genes with strong similar expression patterns and that the found clusters are interpretable.

Keywordsdata mining, bioinformatics, microarray data analysis, clustering
ANZSRC Field of Research 2020490501. Applied statistics
310505. Gene expression (incl. microarray and other genome-wide approaches)
Public Notes

File reproduced in accordance with the copyright policy of the publisher/author.

Byline AffiliationsDepartment of Mathematics and Computing
Department of Biological and Physical Sciences
University of New South Wales
Event18th Australian Joint Conference on Artificial Intelligence
Journal TitleAI 2005: advances in artificial intelligence
Event Details
18th Australian Joint Conference on Artificial Intelligence
Event Date
05 to end of 09 Dec 2005
Event Location
Sydney, Australia
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Nested duplex PCR to detect bordetella pertussis and bordetella parapertussis and its application in diagnosis of pertussis in nonmetropolitan Southeast Queensland, Australia
Farrell, D. J., Daggard, G. and Mukkur, T. K. S.. 1999. "Nested duplex PCR to detect bordetella pertussis and bordetella parapertussis and its application in diagnosis of pertussis in nonmetropolitan Southeast Queensland, Australia." Journal of Clinical Microbiology. 37 (3), pp. 606-610.
Mapping markers for priority traits in the northern grains region of Australia
Mace, E., Sutherland, Mark, Lehmensiek, Anke, Bovill, Bill, Bovill, Jessica, Collard, Bert, Daggard, Grant and Christopher, M. J.. 2006. "Mapping markers for priority traits in the northern grains region of Australia." ITMI Workshop and ACPFG Genomics Symposium (2006). Victor Harbour, Australia 27 - 31 Aug 2006
Mining risk patterns in medical data
Li, Jiuyong, Fu, Ada Wai-Chee, He, Hongxing, Chen, Jie, Jin, Huidong, McAullay, Damien, Williams, Graham, Sparks, Ross and Kelman, Chris. 2005. "Mining risk patterns in medical data." Grossman, R., Bayardo, R., Bennett, K. and Vaidya, J. (ed.) 11th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2005). Chicago, United States 21 - 24 Aug 2005 United States. https://doi.org/10.1145/1081870.1081971
A framework of filtering, clustering and dynamic layout graphs for visualization
Lai, Wei, Huang, Xiaodi and Eades, Peter. 2005. "A framework of filtering, clustering and dynamic layout graphs for visualization." Estivill-Castro, V. (ed.) ACSC 2005: 28th Australasian Computer Science Conference. Newcastle, Australia 28 Jan - 03 Feb 2005 Australia.
Association rule discovery with unbalanced class distributions
Gu, Lifang, Li, Jiuyong, He, Hongxing, Williams, Graham, Hawkins, Simon and Kelman, Chris. 2003. "Association rule discovery with unbalanced class distributions." Gedeon, Tamas D. and Fung, Lance Chun Che (ed.) 16th Australian Conference on Artificial Intelligence (AI 2003). Perth, Australia 03 - 05 Dec 2003 Berlin, Germany. https://doi.org/10.1007/978-3-540-24581-0_19
Mining the optimal class association rule set
Li, Jiuyong, Shen, Hong and Topor, Rodney. 2002. "Mining the optimal class association rule set." Knowledge-Based Systems. 15 (7), pp. 399-405. https://doi.org/10.1016/S0950-7051(02)00024-2
Mining informative rule set for prediction
Li, Jiuyong, Shen, Hong and Topor, Rodney. 2004. "Mining informative rule set for prediction." Journal of Intelligent Information Systems. 22 (2), pp. 155-174. https://doi.org/10.1023/B:JIIS.0000012468.25883.a5
Ticket-based mobile commerce scheme and its implementation
Wang, Hua, Huang, Xiaodi and Dodda, Goutham Reddy. 2006. "Ticket-based mobile commerce scheme and its implementation ." 9th ACM International Symposium on Modeling, Analysis and Simulation of Wireless and Mobile Systems. Terromolinos, Spain 02 - 06 Oct 2006 New York, NY, USA.
Analysis of breast feeding data using data mining methods
He, Hongxing, Jin, Huidong, Chen, Jie, McAullay, Damien, Li, Jiuyong and Fallon, Tony. 2006. "Analysis of breast feeding data using data mining methods." Christen, Peter, Kennedy, Paul J., Li, Jiuyong, Simoff, Simeon J. and Williams, Graham J. (ed.) 5th Australasian Conference on Data Mining and Analystics (AusDM 2006). Sydney, Australia 29 - 30 Nov 2006 Sydney, Australia.
A maximally diversified multiple decision tree algorithm for microarray data classification
Hu, Hong, Li, Jiuyong, Wang, Hua, Daggard, Grant and Shi, Mingren. 2006. "A maximally diversified multiple decision tree algorithm for microarray data classification." Boden, Mikael and Bailey, Timothy (ed.) Workshop on Intelligent Systems for Bioinformatics (2006). Hobart, Australia 04 Dec 2006 Sydney, Australia.
A framework of combining Markov model with association rules for predicting web page accesses
Khalil, Faten, Li, Jiuyong and Wang, Hua. 2006. "A framework of combining Markov model with association rules for predicting web page accesses." Christen, Peter, Kennedy, Paul J., Li, Jiuyong, Simoff, Simeon J. and Williams, Graham J. (ed.) 5th Australasian Conference on Data Mining and Analystics (AusDM 2006). Sydney, Australia 29 - 30 Nov 2006 Canberra, Australia.
A comparative study of classification methods for microarray data analysis
Hu, Hong, Li, Jiuyong, Plank, Ashley, Wang, Hua and Daggard, Grant. 2006. "A comparative study of classification methods for microarray data analysis." Christen, Peter, Kennedy, Paul J., Li, Jiuyong, Simoff, Simeon J. and Williams, Graham J. (ed.) 5th Australasian Conference on Data Mining and Analystics (AusDM 2006). Sydney, Australia 29 - 30 Nov 2006 Canberra, Australia.
(alpha, k)-anonymity: an enhanced k-anonymity model for privacy preserving data publishing
Wong, Raymond Chi-Wing, Li, Jiuyong, Fu, Ada Wai-Chee and Wang, Ke. 2006. "(alpha, k)-anonymity: an enhanced k-anonymity model for privacy preserving data publishing." Eliassi-Rad, Tina, Ungar, Lyle H., Craven, Mark and Gunopulos, Dimitrios (ed.) 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'06). Philadelphia, USA 20 - 23 Aug 2006 New York, USA.
Using multiple and negative target rules to make classifiers more understandable
Li, Jiuyong and Jones, Jason. 2006. "Using multiple and negative target rules to make classifiers more understandable." Knowledge-Based Systems. 19 (6), pp. 438-444. https://doi.org/10.1016/j.knosys.2006.03.003
Current developments of k-anonymous data releasing
Li, Jiuyong, Wang, Hua, Jin, Huidong and Yong, Jianming. 2006. "Current developments of k-anonymous data releasing." Croll, Peter, Morarji, Hasmukh and Au, Richard (ed.) National e-Health Privacy and Security Symposium 2006. Brisbane, Australia 24 - 26 Oct 2006 Brisbane.
Combining gene expression data and gene ontology with the use of a data mining tool
Petrus, Khaleel, Li, Jiuyong and Lopez, J.. 2005. "Combining gene expression data and gene ontology with the use of a data mining tool." Summer Symposium in Bioinformatics: Open Problems in Bioinformatics (BioInfoSummer 2005). Canberra, Australia 28 Nov - 02 Dec 2005 Australian National University (ANU).
A metabolite-deficient mutant of Bordetella pertussis that induces secretory IgA and cell-mediated immunity in mice vaccinated by the intranasal route
Mukkur, T. K. S., Cornford-Nairn, Renee A., Rossetti, T., Kershaw, S., Fry, Scott Robert, Xu, Youhong and Daggard, Grant A.. 2005. "A metabolite-deficient mutant of Bordetella pertussis that induces secretory IgA and cell-mediated immunity in mice vaccinated by the intranasal route." Fang, Ferric C. (ed.) 105th American Society for Microbiology: General Meeting. Atlanta, Georgia 05 - 09 Jun 2005 Washington.
Preparation of total RNA from a very small wheat embryo suitable for differential display
Chen, Yihua, Weining, Song and Daggard, Grant. 2003. "Preparation of total RNA from a very small wheat embryo suitable for differential display ." Annals of Applied Biology. 143 (2), pp. 261-264. https://doi.org/10.1111/j.1744-7348.2003.tb00293.x
Targetting AFLP-DNA markers to specific traits and chromosome regions
Campbell, A. W., Daggard, G., Békés, F., Pedler, A., Sutherland, M. W and Appels, R.. 2001. "Targetting AFLP-DNA markers to specific traits and chromosome regions ." Australian Journal of Agricultural Research. 52 (11-12), pp. 1153-1160. https://doi.org/10.1071/ar01028
Enhanced shoot regeneration in nine Australian wheat cultivars by spermidine and water stress treatments
Khanna, Harjeet K. and Daggard, Grant E.. 2001. "Enhanced shoot regeneration in nine Australian wheat cultivars by spermidine and water stress treatments ." Australian Journal of Plant Physiology. 28 (12), pp. 1243-1247. https://doi.org/10.1071/pp01115