Figure 1.
Venn diagram of the expressed genes along the 4-different tissues (duodenum, jejunum, ileum and ileal Peyer's patches).
Out of the 19,910 expressed genes, 17, 027 genes were co-expressed between tissues. Venn diagram was plotted by using Venny, an interactive tool for comparing lists.
Figure 2.
Multidimensional scaling (MDS) analysis using expression of all normalized genes (n = 12,444); A) Patterns of gene changes along the proximal-distal axis in the small intestine and ileal Peyer's patches; B) Patterns of gene changes along proximal-distal axis in the small intestine.
Plots were performed through the “plotMDS.dge” function of edgeR package in the R statistical environment.
Figure 3.
Euler diagram of ubiquitously differentially expressed genes between tissues.
Euler diagram was implemented through the VennDiagram package in the R statistical environment.
Table 1.
Differential expression results among small intestine segments and Ileal Peyer's patches.
Figure 4.
Molecular and cellular functions significantly modulated when comparing different tissues in Ingenuity Pathway analysis.
Statistical significance was calculated via a right-tailed Fisher's Exact test in Ingenuity. Only molecular and cellular functions that presented a −log P-values exceeding 1.30 (FDR q-values <0.05) were preserved. The colours indicate the different tissue contrasts, and the numbers indicate the genes within each biological function.
Figure 5.
Canonical pathways significantly modulated when comparing different tissues.
Statistical significance of pathway modulation was calculated via a right-tailed Fisher's Exact test in Ingenuity Pathway. Only canonical pathways that presented a −log P-values exceeding 1.30 (FDR q-values <0.05) were preserved. The down-regulated and up-regulated genes for each molecular pathway are presented and the colours indicate the different tissue contrasts.
Figure 6.
IPA networks detected when comparing intestinal tissues relative to the ileum Peyer's patches.
The network included genes involved in Cellular Function and Maintenance, Cellular Assembly and Organization, Infectious Disease and presented a score of 27 and 33 focus genes. The network displayed graphically as nodes (gene/gene products) and edges (the biological relationship between nodes). The node colour intensity indicates the expression of genes: red up-regulated, green down-regulated in intestinal tissues relative to ileal Peyer's patches. The shapes of nodes indicate the functional class of the gene product. The log fold change values are indicated under each node.