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Constructing biological pathways by a two-step counting approach.

Wang H, Lu HH, Chueh TH - PLoS ONE (2011)

Bottom Line: Many approaches have been proposed in the literature to reconstruct biological relationships.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan. wang@stat.nctu.edu.tw

ABSTRACT
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.

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Some pairwise relationships identified by the two-steps counting                            approach (a), and the Li and Lu method (b) using the expression data of                            yeast Saccharomyces cerevisiae.
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pone-0020074-g003: Some pairwise relationships identified by the two-steps counting approach (a), and the Li and Lu method (b) using the expression data of yeast Saccharomyces cerevisiae.

Mentions: The reconstruction results of the DAB network using the two-step approach and the method of Li and Lu [29] are illustrated in Figure 3(a) and Figure 3(b), respectively. In addition, we also implemented the method of Shaoo et al. [27] in this real yeast data. The results show that there are no pair relationships detected by the method of Shaoo et al. [27], because all “” values are smaller than 3 for any two elements. Therefore, compared with the methods in Li and Lu [29] and Shaoo et al. [27], our proposed method is more useful for finding the cascade relationship.


Constructing biological pathways by a two-step counting approach.

Wang H, Lu HH, Chueh TH - PLoS ONE (2011)

Some pairwise relationships identified by the two-steps counting                            approach (a), and the Li and Lu method (b) using the expression data of                            yeast Saccharomyces cerevisiae.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105984&req=5

pone-0020074-g003: Some pairwise relationships identified by the two-steps counting approach (a), and the Li and Lu method (b) using the expression data of yeast Saccharomyces cerevisiae.
Mentions: The reconstruction results of the DAB network using the two-step approach and the method of Li and Lu [29] are illustrated in Figure 3(a) and Figure 3(b), respectively. In addition, we also implemented the method of Shaoo et al. [27] in this real yeast data. The results show that there are no pair relationships detected by the method of Shaoo et al. [27], because all “” values are smaller than 3 for any two elements. Therefore, compared with the methods in Li and Lu [29] and Shaoo et al. [27], our proposed method is more useful for finding the cascade relationship.

Bottom Line: Many approaches have been proposed in the literature to reconstruct biological relationships.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan. wang@stat.nctu.edu.tw

ABSTRACT
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.

Show MeSH