High throughput gene expression profiling by microarray analysis. A. M vs A plot showing genes identified as differentially expressed (2-fold or more, P value ≤ 0.05) between villus and crypt epithelial cells in red. Genes were identified through comparison of median expression levels in 3 independent paraformaldehyde-fixed ileal tissue samples from 3 different individuals. B. Hierarchical clustering of the genes differentially expressed (2-fold or more, P value ≤ 0.05). Common patterns of gene transcription were determined by non-biased clustering analysis, revealing a set of genes whose expression was enriched in each of the 2 lineages, villus and crypt epithelial cells. C. Pathway analysis of the differentially expressed genes reveals physiological processes that predominate the biology of villus and crypt epithelial cell lineages. Genes enriched in the 2 lineages evaluated were analyzed statistically to determine which pathways and processes were most represented each cell type. The top 5 pathways/processes implicated for each lineage are shown.