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Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle

Chen, Qingfeng and Chen, Yi-Ping Phoebe 2006, Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle, BMC bioinformatics, vol. 7, no. 394, pp. 1-14.

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Title Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle
Author(s) Chen, Qingfeng
Chen, Yi-Ping Phoebe
Journal name BMC bioinformatics
Volume number 7
Issue number 394
Start page 1
End page 14
Publisher BioMed Central Ltd
Place of publication London, England
Publication date 2006
ISSN 1471-2105
Keyword(s) hydroxymethylglutaryl coenzyme A reductase kinase
isoenzyme
alpha chain
Summary Background
AMP-activated protein kinase (AMPK) has emerged as a significant signaling intermediary that regulates metabolisms in response to energy demand and supply. An investigation into the degree of activation and deactivation of AMPK subunits under exercise can provide valuable data for understanding AMPK. In particular, the effect of AMPK on muscle cellular energy status makes this protein a promising pharmacological target for disease treatment. As more AMPK regulation data are accumulated, data mining techniques can play an important role in identifying frequent patterns in the data. Association rule mining, which is commonly used in market basket analysis, can be applied to AMPK regulation.

Results
This paper proposes a framework that can identify the potential correlation, either between the state of isoforms of α, β and γ subunits of AMPK, or between stimulus factors and the state of isoforms. Our approach is to apply item constraints in the closed interpretation to the itemset generation so that a threshold is specified in terms of the amount of results, rather than a fixed threshold value for all itemsets of all sizes. The derived rules from experiments are roughly analyzed. It is found that most of the extracted association rules have biological meaning and some of them were previously unknown. They indicate direction for further research.

Conclusion
Our findings indicate that AMPK has a great impact on most metabolic actions that are related to energy demand and supply. Those actions are adjusted via its subunit isoforms under specific physical training. Thus, there are strong co-relationships between AMPK subunit isoforms and exercises. Furthermore, the subunit isoforms are correlated with each other in some cases. The methods developed here could be used when predicting these essential relationships and enable an understanding of the functions and metabolic pathways regarding AMPK.
Language eng
Field of Research 080610 Information Systems Organisation
Socio Economic Objective 970108 Expanding Knowledge in the Information and Computing Sciences
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ┬ęThis is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Persistent URL http://hdl.handle.net/10536/DRO/DU:30003611

Document type: Journal Article
Collections: School of Engineering and Information Technology
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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.