We have recently demonstrated that nutritional bioactives (fish oil and pectin) 
modulate microRNA molecular switches in the colon. Since integrated analysis of 
microRNA and mRNA expression at an early stage of colon cancer development is 
lacking, in this study, four computational approaches were utilized to test the 
hypothesis that microRNAs and their posttranscriptionally regulated mRNA 
targets, i.e., both total mRNAs and actively translated mRNA transcripts, are 
differentially modulated by carcinogen and diet treatment. Sprague-Dawley rats 
were fed diets containing corn oil ± fish oil with pectin ± cellulose and 
injected with azoxymethane or saline (control). Colonic mucosa was assayed at an 
early time of cancer progression, and global gene set enrichment analysis was 
used to obtain those microRNAs significantly enriched by the change in 
expression of their putative target genes. In addition, cumulative distribution 
function plots and functional network analyses were used to evaluate the impact 
of diet and carcinogen combination on mRNA levels induced via microRNA 
alterations. Finally, linear discriminant analysis was used to identify the best 
single-, two-, and three-microRNA combinations for classifying dietary effects 
and colon tumor development. We demonstrate that polysomal profiling is tightly 
related to microRNA changes when compared with total mRNA profiling. In 
addition, diet and carcinogen exposure modulated a number of microRNAs (miR-16, 
miR-19b, miR-21, miR26b, miR27b, miR-93, and miR-203) linked to canonical 
oncogenic signaling pathways. Complementary gene expression analyses showed that 
oncogenic PTK2B, PDE4B, and TCF4 were suppressed by the chemoprotective diet at 
both the mRNA and protein levels.