Closer integration of biological knowledge of genes with the analysis of expression data can enable more detailed examination of the patient samples.
Gene Ontology (GO) [8] and Kyoto Encyclopedia of Genes and Genomes (KEGG) [9] are the two main annotation databases collecting biological knowledge of genes, which make them very suitable for bioinformatics scanning for enrichment analysis [6].
This process takes advantage of biological knowledge of gene-gene relationships rather than requiring loci to have demonstrated a main effect, allowing for the detection of those variants that are only found to be associated with a given phenotype when acting in combination with another locus.
It is increasingly recognized that pathway analysis can support exploration of genome-wide association study (GWAS) data by incorporating the available biological knowledge of genes and pathways.
Given the freedom of assigning weights to p-values, weighted FDR provides an excellent platform to incorporate expert biological knowledge of each gene's biological function.
Prior probability is likely to be influenced by the biological knowledge of the gene, the functional significance of the variants and the available epidemiological evidence.
Given this commonality of function among genes that show age-related changes in expression, we decided to investigate aging-dependent gene expression in the context of biological knowledge of the function of genes, as provided by pathway annotations.
In this Bayesian framework, priors incorporate biological knowledge of interactions between TFs and target genes.
Network analysis provides a framework to search for communities of genes associated with disease by modeling their coordinated behavior and biological knowledge of their interactions.
But the gene interaction networks found are at least under the sanction of current biological knowledge of transcription factors to the reasonable extent.
