TreeDT : tree pattern mining for gene mapping

Show full item record



Permalink

http://hdl.handle.net/10138/143994

Citation

Sevon , P , Toivonen , H & Ollikainen , V 2006 , ' TreeDT : tree pattern mining for gene mapping ' , IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol. 3 , no. 2 , pp. 174-185 .

Title: TreeDT : tree pattern mining for gene mapping
Author: Sevon, Petteri; Toivonen, Hannu; Ollikainen, Vesa
Contributor: University of Helsinki, Department of Computer Science
University of Helsinki, Department of Computer Science
Date: 2006
Language: eng
Number of pages: 12
Belongs to series: IEEE/ACM Transactions on Computational Biology and Bioinformatics
ISSN: 1545-5963
URI: http://hdl.handle.net/10138/143994
Abstract: We describe TreeDT, a novel association-based gene mapping method. Given a set of disease-associated haplotypes and a set of control haplotypes, TreeDT predicts likely locations of a disease susceptibility gene. TreeDT extracts, essentially in the form of haplotype trees, information about historical recombinations in the population: A haplotype tree constructed at a given chromosomal location is an estimate of the genealogy of the haplotypes. TreeDT constructs these trees for all locations on the given haplotypes and performs a novel disequilibrium test on each tree: Is there a small set of subtrees with relatively high proportions of disease-associated chromosomes, suggesting shared genetic history for those and a likely disease gene location? We give a detailed description of TreeDT and the tree disequilibrium tests, we analyze the algorithm formally, and we evaluate its performance experimentally on both simulated and real data sets. Experimental results demonstrate that TreeDT has high accuracy on difficult mapping tasks and comparisons to other methods (EATDT, HPM, TDT) show that TreeDT is very competitive.
Subject: 113 Computer and information sciences
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
treedt_tcbb_06.pdf 1.269Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record