• Documents
  • Authors
  • Tables
  • Log in
  • Sign up
  • MetaCart
  • DMCA
  • Donate

CiteSeerX logo

Advanced Search Include Citations
Advanced Search Include Citations

Mining subspace clusters from DNA microarray data using large itemset techniques (2009)

by Y I Chang, J R Chen, Y C Tsai
Venue:J. Comput. Biol
Add To MetaCart

Tools

Sorted by:
Results 1 - 1 of 1

An Up-Down Bit Pattern Approach to Coregulated and Negative-Coregulated Gene Clustering of Microarray Data

by Jiun-rung Chen, Ye-in Chang
"... Biclustering, which performs simultaneous clustering of rows (e.g., genes) and columns (e.g., conditions), has been shown to be important for analyzing microarray data. To find biclusters, there have been many methods proposed. Most of these methods can find only clusters with coregulated patterns, ..."
Abstract - Add to MetaCart
Biclustering, which performs simultaneous clustering of rows (e.g., genes) and columns (e.g., conditions), has been shown to be important for analyzing microarray data. To find biclusters, there have been many methods proposed. Most of these methods can find only clusters with coregulated patterns, which means that the expression levels of genes in a found cluster rise and fall simultaneously. However, for real microarray data, there exist negative-correlated patterns, which means that the tendencies of expression levels of some genes may be completely inverse to those of the other genes under some conditions. Although one method called Co-gclustering was proposed to simultaneously find clusters with cor-related and negative-correlated patterns, its time complexity is exponential to the number of conditions, which may not be efficient. Therefore, in this article, we propose a new method, Up-Down Bit pattern (UDB), to efficiently find clusters with correlated and negative-correlated patterns. First, we utilize up-down bit patterns to record those condition pairs where one gene is upregulated or downregulated. One gene is upregulated (or down-regulated) under condition pair a and b if its expression level shows an upward (or down-ward) tendency from condition a to condition b. Then, we apply a heuristic idea on these up-down bit patterns to efficiently find clusters, which will reduce the time complexity from exponential time to polynomial time. From the experimental results, we show that the UDB method is more efficient than the Co-gclustering method. Key words: cluster, coregulation, microarray, negative-correlated pattern. 1.
(Show Context)

Citation Context

...e full space, i.e., all conditions, and Figure 1b shows a bicluster of 2 genes with coherent values on only the subspace, i.e., conditions a, b, c, and e. Methods for biclusters with coherent values (=-=Chang et al., 2009-=-; Cheng and Church, 2000; Wang et al., 2002; Yoon et al., 2005; Zhao and Zaki, 2005) aim to cluster those genes whose expression values have simple linear transformation relationships. Genes in such a...

Powered by: Apache Solr
  • About CiteSeerX
  • Submit and Index Documents
  • Privacy Policy
  • Help
  • Data
  • Source
  • Contact Us

Developed at and hosted by The College of Information Sciences and Technology

© 2007-2019 The Pennsylvania State University