標題: Constructing Biological Pathways by a Two-Step Counting Approach
作者: Wang, Hsiuying
Lu, Henry Horng-Shing
Chueh, Tung-Hung
統計學研究所
Institute of Statistics
公開日期: 1-六月-2011
摘要: Networks are widely used in biology to represent the relationships between genes and gene functions. In Boolean biological models, it is mainly assumed that there are two states to represent a gene: on-state and off-state. It is typically assumed that the relationship between two genes can be characterized by two kinds of pairwise relationships: similarity and prerequisite. Many approaches have been proposed in the literature to reconstruct biological relationships. In this article, we propose a two-step method to reconstruct the biological pathway when the binary array data have measurement error. For a pair of genes in a sample, the first step of this approach is to assign counting numbers for every relationship and select the relationship with counting number greater than a threshold. The second step is to calculate the asymptotic p-values for hypotheses of possible relationships and select relationships with a large p-value. This new method has the advantages of easy calculation for the counting numbers and simple closed forms for the p-value. The simulation study and real data example show that the two-step counting method can accurately reconstruct the biological pathway and outperform the existing methods. Compared with the other existing methods, this two-step method can provide a more accurate and efficient alternative approach for reconstructing the biological network.
URI: http://dx.doi.org/10.1371/journal.pone.0020074
http://hdl.handle.net/11536/23124
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0020074
期刊: PLOS ONE
Volume: 6
Issue: 6
結束頁: 
顯示於類別:期刊論文


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  1. 000291309900001.pdf