Background: The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just several hundred pathways, but also can increase the explanatory power for the experiment by identifying active pathways in different conditions. However, current approaches are designed to analyze a biological system assuming that each pathway is independent of the other pathways. Results: A decision analysis model is developed in this article that accounts for dependence among pathways in time-course experiments and multiple treatments experiments. This model introduces a decision coefficient—a designed index, to identify the most relevant pathways in a given experiment by taking into account not only the direct determination factor of each Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway itself, but also the indirect determination factors from its related pathways. Meanwhile, the direct and indirect determination factors of each pathway are employed to demonstrate the regulation mechanisms among KEGG pathways, and the sign of decision coefficient can be used to preliminarily estimate the impact direction of each KEGG pathway. The simulation study of decision analysis demonstrated the application of decision analysis model for KEGG pathway analysis. Conclusions: A microarray dataset from bovine mammary tissue over entire lactation cycle was used to further illustrate our strategy. The results showed that the decision analysis model can provide the promising and more biologically meaningful results. Therefore, the decision analysis model is an initial attempt of optimizing pathway analysis methodology.

In order to evaluate ecological technology scientifically, we constructed a modular “three-stage evaluation method” based on qualitative evaluation, semiquantitative evaluation and quantitative evaluation, and established the theoretical models of the four kinds of ecotechnology, such as soil and water conservation technology, desertification governance technology, rocky desertification governance technology and ecological restoration technology. We gave the quantification criteria of the first-level and second-level index commonly shared by four kinds of ecotechnology and defined the quantification criteria of the third-level index of reflecting the heterogeneity of soil and water conservation technology. An ecotechnology evaluation model combining Analytic Hierarchy Process and Logistic regression was established based on soil and water conservation technology. The rationality of the evaluation method and model were verified by field investigation data of soil and water conservation technology in Gaoxigou. The evaluation method and model could provide scientific basis for the effective introduction and popularization of ecotechnology.