Proceedings Article10.1145/1244002.1244032
Exploiting inter-gene information for microarray data integration
Kuan-ming Lin,Jaewoo Kang +1 more
- 11 Mar 2007
- pp 123-127
5
TL;DR: This paper proposes a formal data model for microarray integration using inter-gene information and effective filtering, which generalizes the previous two frameworks and shows how the proposed model can handle a broader range of problems than the previous frameworks.
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Abstract: Microarray data integration is an important yet challenging problem. Usually, direct integration of microarrays after normalization is ineffective because of the diverse types of experiment specific variations. To address this issue, two novel integration approaches were proposed in recent microarray studies. The first study[16] presented a cancer classification technique which identifies gene pairs whose expression orders are consistent within class and different across classes. The other study[18] presented a promising gene expression analysis technique which utilizes pairwise correlations of gene expressions across different microarray datasets. Interestingly, we observe that both of the independently developed techniques rely on inter-gene information and noise filtering strategy to achieve satisfactory performance in microarray integration. Motivated by this observation, we propose in this paper a formal data model for microarray integration using inter-gene information and effective filtering, which generalizes the previous two frameworks. We also show how the proposed model can handle a broader range of problems than the previous frameworks.
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Citations
A Hybrid DTW Based Method for Integration Analysis of Time Series Data
Veselka Boeva,Elena Kostadinova +1 more
- 24 Sep 2009
TL;DR: A new hybrid method is proposed, which is specially suited for integration analysis of time series expression data across different experiments, and validated on gene expression time series data coming from two independent studies examining the global cell-cycle control of gene expression in fission yeast Schizosaccharomyces pombe.
8
A cube framework for incorporating inter-gene information into biological data mining
Kuan-ming Lin,Jaewoo Kang,Hanjun Shin,Jusang Lee +3 more
- 01 Mar 2009
TL;DR: This work proposes a new microarray integration framework that achieves high-quality integration through exploiting invariant features such as relative information among genes and shows how the proposed approach generalises the previous frameworks.
5
Microarray data analysis with PCA in a DBMS
Waree Rinsurongkawong,Carlos Ordonez +1 more
- 30 Oct 2008
TL;DR: This work adapts the Householder tridiagonalization and QR factorization numerical methods to solve SVD inside the DBMS, and achieves processing times comparable with those from the R package, a well-known statistical tool.
An adaptive approach for integration analysis of multiple gene expression datasets
Veselka Boeva,Elena Kostadinova +1 more
- 08 Sep 2010
TL;DR: This paper investigates how to integrate microarray data coming from different studies for the purpose of gene dependence analysis, and proposes a method for direct integration analysis of gene relationships across different experiments and platforms.
2
Exploiting Inter-Sample Information and Exploring Visualization in Data Mining: from Bioinformatics to Anthropology and Aesthetics Disciplines
Kuan-Ming Lin,Jung-Hua Liu +1 more
- 21 Jan 2011
TL;DR: This chapter presents recent achievements in applying data mining techniques to two application areas— microarray analysis and anthropology study on Wi-Fi networks— and applies visualization techniques to help integrate heterogeneous databases to obtain useful data interpretation.
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