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

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.

Mining frequent itemsets for protein kinase regulation

Protein kinases, a family of enzymes, have been viewed as an important signaling intermediary by living organisms for regulating critical biological processes such as memory, hormone response and cell growth. The
unbalanced kinases are known to cause cancer and other diseases. With the increasing efforts to collect, store and disseminate information about the entire kinase family, it not only leads to valuable data set to understand cell regulation but also poses a big challenge to extract valuable knowledge about metabolic pathway from the data. Data mining techniques that have been widely used to find frequent patterns in large datasets can be extended and adapted to kinase data as well. This paper proposes a framework for mining frequent itemsets from the collected kinase dataset. An experiment using AMPK regulation data demonstrates that our approaches are useful and efficient in analyzing kinase regulation data.

Mining small databases by collecting knowledge

Current data mining techniques may not be helpful for mining some companies/organizations such as nuclear power plants and earthquake bureaus, which have only small databases. Apparently, these companies/organizations also expect to apply data mining techniques to extract useful patterns in their databases so as to make their decisions. However, data in these databases such as the accident database of a nuclear power plant and the earthquake database in an earthquake bureau, may not be large enough to form any patterns. To meet the applications, we present a new mining model in this paper, which is based on the collecting knowledge from such as Web, journals, and newspapers.

Collecting quality data for database mining

Data collecting is necessary to some organizations such as nuclear power plants and earthquake bureaus, which have very small databases. Traditional data collecting is to obtain necessary data from internal and external data-sources and join all data together to create a homogeneous huge database. Because collected data may be untrusty, it can disguise really useful patterns in data. In this paper, breaking away traditional data collecting mode that deals with internal and external data equally, we argue that the first step for utilizing external data is to identify quality data in data-sources for given mining tasks. Pre- and post-analysis techniques are thus advocated for generating quality data.

An web content based data mining for car consumption in China

This paper introduces an incremental FP-Growth approach for Web content based data mining and its application in solving a real world problem The problem is solved in the following ways. Firstly, we obtain the semi-structured data from the Web pages of Chinese car market and structure them and save them in local database. Secondly, we use an incremental FP-Growth algorithm for mining association rules to discover Chinese consumers' car consumption preference. To find more general regularities, an attribute-oriented induction method is also utilized to find customer's consumption preference among a range of car categories. Experimental results have revealed some interesting consumption preferences that are useful for the decision makers to make the policy to encourage and guide car consumption. Although the current data we used may not be the best representative of the actual market in practice, it is still good enough for the decision making purpose in terms of reflecting the real situation of car consumption preference under the two assumptions in the context.

Software warehouse and software mining : the impact of data mining to software engineering

Automating Software Engineering is the dream of software Engineers for decades. To make this dream to come to true, data mining can play an important role. Our recent research has shown that to increase the productivity and to reduce the cost of software development, it is essential to have an effective and efficient mechanism to store, manage and utilize existing software resources, and thus to automate software analysis, testing, evaluation and to make use of existing software for new problems. This paper firstly provides a brief overview of traditional data mining followed by a presentation on data mining in broader sense. Secondly, it presents the idea and the technology of software warehouse as an innovative approach in managing software resources using the idea of data warehouse where software assets are systematically accumulated, deposited, retrieved, packaged, managed and utilized driven by data mining and OLAP technologies. Thirdly, we presented the concepts and technology and their applications of data mining and data matrix including software warehouse to software engineering. The perspectives of the role of software warehouse and software mining in modern software development are addressed. We expect that the results will lead to a streamlined high efficient software development process and enhance the productivity in response to modern challenges of the design and development of software applications.