Fig 1.
Schematic diagram showing the study experimental design, the integrative computational analysis, and the validation procedures used in this study.
See Fig 2 for the list of comparisons conducted between the pairs of samples.
Fig 2.
Venn diagrams showing overlapping differentially expressed genes among the six comparisons.
(A) Comparisons 1–5, (B) comparisons 1–4 and 6. In both Venn diagrams the same 80 genes were found specific to comparison 4 (non-diabetic EPCs vs D-EPCs).
Fig 3.
Heat maps of the microarray analysis results.
(A): Differentially expressed genes in all 36 samples. Green-spots represent down-regulated genes, and red-spots represent up-regulated genes. The blue color represents D-EPCs, the orange color represents the non-diabetic EPCs, the blue pink represents diabetic Lin+, and the gray color represents the non-diabetic Lin+. (B): 80 core enrichment genes in comparison-4 (non-diabetic vs D-EPCs). Green spots represent down-regulated genes, and red spots represent up-regulated genes. The order of genes is obtained by hierarchical clustering. The orange color represents the non-diabetic EPCs while the blue color represents the D-EPCs.
Fig 4.
Six interesting co-regulatory motifs suggesting a cooperative functional role between the identified central-hubs and their potential partners of miRNAs, TFs, and target genes in the D-EPC-GRN network.
TFs are represented by a turquoise triangle whereas miRNAs are shown as orange squares. Pink nodes denote the common target genes and the grey nodes depict the co-regulated genes.
Fig 5.
Functional homogeneity of the visualized six motifs.
Cumulative distribution of GO functional semantic scores of gene pairs of co-regulated genes in the examined six motifs (red) versus randomly selected genes (black). The p-value was calculated using the Kolmogorov-Smirnov test.
Fig 6.
Visualization of all motifs that include mir-139-5p and its interactions with central-hubs.