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Gene duplications provide a means to evolve novel biological functions, and changes in protein functions may then yield different evolutionary constraints on duplicated genes [40].
Gene duplication provide a means to evolve novel biological functions and changes in protein functions may then provide different evolutionary constraints on duplicated genes.
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They were selected for investigation based on their interesting biological functions and high fold-changes, as well as the availability of commercial antibodies.
This type of approach brings robust information about the relationship between biological function and physiological changes.
This analysis examined genes in the selected modules that are known to affect biological functions and compared their direction of change (i.e. expression in cluster E samples relative to cluster I) to that expected from the literature.
IPA could determine the biological functions and diseases from the significantly changed expression levels of groups of genes: 733 molecules were found to be involved in cancer development, 567 in cellular growth and proliferation, 552 in cellular development, 520 in cell death and survival and 402 in gastrointestinal diseases.
Significant differential expression was determined in genes with FDR-adjusted p-values < 0.05 and fold change ± 2. Biological functions and interactions of the genes differentially expressed were determined using the database for annotation visualization and integrated discovery (DAVID v6.7) and the Ingenuity pathway analysis (IPA) (Ingenuity® Systems).
These proteins were selected on the basis of interesting biological function and high fold-change, as well as availability of commercial antibodies.
IPA software calculates a Benjamini & Hochberg-adjusted p-value for the association of protein abundance changes with each biological function, and a weighted z-score, which estimates whether the protein abundance changes found associated with a specific biological function are likely to enhance (positive z values) or inhibit (negative) the function.
Genes were further analyzed by Ingenuity Pathway Analyses to relate age-associated gene expression changes to biological function and signaling pathways.
To further characterize these genomic changes according to biological function and identify molecular pathways involved in the mode of action of each chemical, these gene lists were uploaded into GenMAPP (Gene Map Annotator and Pathway Profiler, version 1.0; Dahlquist et al. 2002).
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