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No relationship between the specified pathways simplifies the correction for multiple hypothesis testing.
Pathways listed are identified enriched pathways for indicated phenotypes; numbers in square brackets indicate the Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers for specified pathways.
Traditional forms of microarray analysis result in long lists of significant differentially expressed genes or arbitrarily specified pathways and do not consider differential co-expression dynamics; rather they only focus on mean expression levels.
The complexity of the response required a system-wide approach to data analysis, so the MetaCore™ software (GeneGo, Inc., St. Joseph, MI, USA) was used to assess the significance of changes in expression of genes in specified pathways [ 70, 71].
The model proposed by Wallander and Varni allows the identification of modifiable risk and protective factors in patients' adjustment by testing specified pathways (1) with a clear description of the role of disease-related and psychosocial factors.
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The genes in the specified pathway are graphically represented as a color-coded diagram.
R i is the rank of the ith gene of the specified pathway in a list, r i is the absolute correlation value r.
ParaRate is similarly defined as the total number of corresponding paralogous genes within a specified pathway from the query species divided by the total number of associated genes within the identical pathway from the reference species.
OrthRate is defined as the total number of corresponding orthologous genes within a specified pathway from the query species divided by the total number of associated genes within the identical pathway from the reference species.
On the basis of these strategies, we suggest a model specifying pathways to effect.
Thus, the network is established without explicitly specifying pathways.
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