ABSTRACT
The pathway information in KEGG and the chromosome location in LocusLink, and three different similarity measurements are used to analyze the similarity of the mRNA expression level of genes which have strong correlative function with each other in a pathway and have near location with each other in the chromosome. The results are summarized as follows: (1) Quite a number of genes show significant correlation with other correlative genes at mRNA expression level. (2) The mRNA expression level is consistent with the intensity of functional relationships between genes. So it can be concluded that the function of genes involved in any pathway is correlated with the mRNA expression level of genes.
Subject(s)
Humans , Adenocarcinoma , Genetics , Chromosome Mapping , Methods , Colonic Neoplasms , Genetics , Databases, Genetic , Gene Expression Profiling , Methods , Gene Expression Regulation, Neoplastic , Oligonucleotide Array Sequence Analysis , Methods , RNA, Messenger , MetabolismABSTRACT
Objective: To develop novel strategies to identify relevant molecular signatures for complex human diseases based on data of identical-by-decent profiles and genomic context.Methods: In the proposed strategies, we define four relevancy criteria for mapping SNP-phenotype relationships-point-wise IBD mean difference, averaged IBD difference for window, Z curve and averaged slope for window.Results: Application of these criteria and permutation test to 100 simulated replicates for two hypothetical American populations to extract the relevant SNPs for alcoholism based on sib-pair IBD profiles of pedigrees demonstrates that the proposed strategies have successfully identified most of the simulated true loci.Conclusion: The data mining practice implies that IBD statistic and genomic context could be used as the informatics for locating the underlying genes for complex human diseases. Compared with the classical Haseman-Elston sib-pair regression method, the proposed strategies are more efficient for large-scale genomic mining.