Discovering classes in microarray data using island counts

Brendan Mumey (), Louise Showe and Michael Showe
Additional contact information
Brendan Mumey: Montana State University
Louise Showe: The Wistar Institute
Michael Showe: The Wistar Institute

Journal of Combinatorial Optimization, 2007, vol. 13, issue 3, No 2, 207-216

Abstract: Abstract We present a new biclustering algorithm to simultaneously discover tissue classes and identify a set of genes that well-characterize these classes from DNA microarray data sets. We employ a combinatorial optimization approach where the object is to simultaneously identify an interesting set of genes and a partition of the array samples that optimizes a certain score based on a novel color island statistic. While this optimization problem is NP-complete in general, we are effectively able to solve problems of interest to optimality using a branch-and-bound algorithm. We have tested the algorithm on a 30 sample Cutaneous T-cell Lymphoma data set; it was able to almost perfectly discriminate short-term survivors from long-term survivors and normal controls. Another useful feature of our method is that can easily handle missing expression data.

Keywords: Microarrays; Biclustering; Class discovery (search for similar items in EconPapers)
Date: 2007
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
http://link.springer.com/10.1007/s10878-006-9021-9 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:spr:jcomop:v:13:y:2007:i:3:d:10.1007_s10878-006-9021-9

Ordering information: This journal article can be ordered from
https://www.springer.com/journal/10878

DOI: 10.1007/s10878-006-9021-9

Access Statistics for this article

Journal of Combinatorial Optimization is currently edited by Thai, My T.

More articles in Journal of Combinatorial Optimization from Springer
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().