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Constrained query of order-preserving submatrix in gene expression data

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Abstract

Order-preserving submatrix (OPSM) has become important in modelling biologically meaningful subspace cluster, capturing the general tendency of gene expressions across a subset of conditions. With the advance of microarray and analysis techniques, big volume of gene expression datasets and OPSM mining results are produced. OPSM query can efficiently retrieve relevant OPSMs from the huge amount of OPSM datasets. However, improving OPSM query relevancy remains a difficult task in real life exploratory data analysis processing. First, it is hard to capture subjective interestingness aspects, e.g., the analyst’s expectation given her/his domain knowledge. Second, when these expectations can be declaratively specified, it is still challenging to use them during the computational process of OPSM queries. With the best of our knowledge, existing methods mainly focus on batch OPSM mining, while few works involve OPSM query. To solve the above problems, the paper proposes two constrained OPSM query methods, which exploit userdefined constraints to search relevant results from two kinds of indices introduced. In this paper, extensive experiments are conducted on real datasets, and experiment results demonstrate that the multi-dimension index (cIndex) and enumerating sequence index (esIndex) based queries have better performance than brute force search.

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Authors and Affiliations

  1. School of Computer Science and Technology, Northwestern Polytechnical University, Xi’an, 710072, China

    Tao Jiang, Zhanhuai Li, Xuequn Shang, Bolin Chen, Weibang Li & Zhilei Yin

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  1. Tao Jiang
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  2. Zhanhuai Li
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  3. Xuequn Shang
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  4. Bolin Chen
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  5. Weibang Li
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  6. Zhilei Yin
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Corresponding author

Correspondence to Zhanhuai Li.

Additional information

Tao Jiang is a PhD candidate at School of Computer Science and Technology, Northwestern Polytechnical University, China. He is a student member of China Computer Federation, Association for Computing Machinery, and IEEE Computer Society. His current research interests include biological data mining, big data analysis, and data management.

Zhanhuai Li is a professor at School of Computer Science and Technology, Northwestern Polytechnical University (NWPU), China. He is vice chairman of Database Technical Committee, China Computer Federation. He received his MS and PhD degrees from NWPU. His research interests include data management and data mining.

Xuequn Shang is a professor and vice dean at School of Computer Science and Technology, Northwestern Polytechnical University, China. She is a senior member of China Computer Federation. She received her PhD degree from University of Magdeburg, Germany in 2005. Her current research interests include data mining, bioinformatics, and data management.

Bolin Chen is an associate professor at School of Computer Science and Technology, Northwestern Polytechnical University, China. He received his PhD degree from University of Saskatchewan, Saskatoon, Canada. His current research interests include bioinformatics, computational and systems biology, data mining, and data management.

Weibang Li is a PhD candidate of the School of Computer Science and Technology, Northwestern Polytechnical University, China. He received his BS degree from Nanjing University of Aeronautics and Astronautics, China in 2003. His current research interests include data quality management, big data analysis, and cloud computing.

Zhilei Yin is a PhD candidate of the School of Computer Science and Technology, Northwestern Polytechnical University, China. He is a lecturer of Zhengzhou University of Light Industry, China. His current research interests include bioinformatics, data mining, database management, and machine learning.

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Jiang, T., Li, Z., Shang, X. et al. Constrained query of order-preserving submatrix in gene expression data. Front. Comput. Sci. 10, 1052–1066 (2016). https://doi.org/10.1007/s11704-016-5487-5

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  • DOI: https://doi.org/10.1007/s11704-016-5487-5

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