title: Constructing biological pathways by a two-step counting approach.
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.
authors.affiliation: Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan. wang@stat.nctu.edu.tw
authors.forename: Hsiuying
authors.initials: H
authors.lastname: Wang
authors.forename: Henry Horng-Shing
authors.initials: HH
authors.lastname: Lu
authors.forename: Tung-Hung
authors.initials: TH
authors.lastname: Chueh
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling; D020935:MAP Kinase Signaling System; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics