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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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Diagram of a directed acyclic Boolean network with seven elements and                        twelve pair relationships.Only arrows between covering pairs are shown.
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pone-0020074-g002: Diagram of a directed acyclic Boolean network with seven elements and twelve pair relationships.Only arrows between covering pairs are shown.

Mentions: To describe the model and notations, we adopted a simple example used in Li and Lu [29] to illustrate the model assumption. Figure 2 shows the relationships of the seven elements in this example derived from the 13 states of Table 1. In the diagram, the notation denotes that A is a prerequisite of B and the notation denotes that B and E are similar. Note that in Figure 2 are called elements. The definitions of prerequisite and similar relationships for any two elements and are defined as follows.


Constructing biological pathways by a two-step counting approach.

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

Diagram of a directed acyclic Boolean network with seven elements and                        twelve pair relationships.Only arrows between covering pairs are shown.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020074-g002: Diagram of a directed acyclic Boolean network with seven elements and twelve pair relationships.Only arrows between covering pairs are shown.
Mentions: To describe the model and notations, we adopted a simple example used in Li and Lu [29] to illustrate the model assumption. Figure 2 shows the relationships of the seven elements in this example derived from the 13 states of Table 1. In the diagram, the notation denotes that A is a prerequisite of B and the notation denotes that B and E are similar. Note that in Figure 2 are called elements. The definitions of prerequisite and similar relationships for any two elements and are defined as follows.

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