After applying these measures to generate a synthetic network, we searched for likely connections between Apc and Cdkn1a using both gene coexpression data and Gene Ontology association rules.
In fact, gene coexpression data are extensively used for gene targeting in Arabidopsis research, whereas this is not a major approach used in mammalian studies.
Gene coexpression data has been used in the design of a wide variety of experiments, such as gene targeting, regulatory investigations and identification of potential partners in protein protein interactions (Aoki et al., 2007; Shoemaker and Panchenko, 2007).
To calculate condition-independent gene coexpression data, we constructed gene expression profiles using as many genes and samples as possible.
To easily extract pertinent information from gene coexpression data, gene coexpression databases with various analysing tools have been constructed for model organisms.
The focus of our assessment was to obtain more information from gene coexpression data.
Our results provide a standard calculation procedure for condition-independent gene coexpression data to elucidate gene-to-gene functional relationships.
Condition-independent gene coexpression data are constructed based on hundreds or thousands of GeneChip data to generalize specific experimental conditions; for example, for Arabidopsis, 1310, 1779 and 1388 GeneChips are used for PED, CressExpress and ATTED-II, respectively.
MRFSeq [ 12] combines a Markov random field (MRF) model and the gene coexpression data to predict differential gene expression.
By integrating our GWAS findings with eSNP, coexpression, and pathway analyses using gene expression data from disease-relevant tissue generated from subjects who had undergone GWAS, we tested the potential biologic context of our GWAS findings through integrative methods and identified a novel pathway in allergic rhinitis mitochondrial pathways.
