Title: A parallel approach toward correlation measurement for gene pairs with time-lagging expression behaviours

Authors: Xiaopeng (Leon) Cao, Mengxia Zhu

Addresses: Computer Science Department, Southern Illinois University, Carbondale, Carbondale, IL 62901, USA. ' Computer Science Department, Southern Illinois University, Carbondale, Carbondale, IL 62901, USA

Abstract: Time-lagging in expression occurs when a gene|s expression triggers a delayed expression in its co-regulated or anti-co-regulated peers. Arbitrary time-lagging also might appear due to experiment or measurement error. Traditional methods will either under-estimate or completely miss such correlation, which is not unusual and plays important roles. Since the traditional similarity measurement cannot capture the true relationship, a simple time-lagging captured algorithm integrated with some existing time-lagging and similarity measurement techniques is proposed with parallel implementation. Improvements such as isolation of experimental conditions and weighted averages are used to achieve better accuracy and give user flexibility to differentiate different experiments.

Keywords: microarrays; correlation measurement; time lagging; dynamic programming; parallel computing; gene pairs; expression behaviours; gene expression.

DOI: 10.1504/IJCBDD.2009.030118

International Journal of Computational Biology and Drug Design, 2009 Vol.2 No.3, pp.278 - 287

Published online: 10 Dec 2009 *

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