Table 1.
Demographic characteristics of infant and adult subjects.
Fig 1.
A. PCA plot showing adult groups, infants and infant anatomical sites. PCA plot shows Adults 20s (red squares), Adults 60s (blue squares), and Infants (green symbols). Within the infant cluster, anatomical sites are shown with different symbols (circle indicates abdomen, triangle indicates back, cross indicates chest). Clear separation in gene expression is observed for infant versus adult skin. The effect of gender is shown in Fig 1B, indicating strong separation between adults. B. PCA plot showing adult groups, infants and infants by sex. The PCA plot shows Adults 20s (red circles), Adults 60s (blue circles) and Infants (green symbols). Within the infant cluster, female sex is shown as circle and male sex as triangles. No strong separation in gene expression is observed in the infant cluster based on sex.
Fig 2.
Hierarchical clustering analysis of differentially expressed genes in full-thickness skin tissue for infants and adults.
A. Heatmap showing samples with normalized expression values (based on z-score) of all 1,086 differentially regulated genes with adjusted P value <0.05 and absolute fold change > = 1.5 for infant and adult (A20s: 20 years old, A60s: 60years old) Euclidean distances between each sample were calculated, and an unsupervised hclust algorithm was used for clustering analysis. Samples formed 2 clusters clearly separating infants (pink) and adults (blue, all adults; purple, 20 years; green, 60 years). Genes were grouped for similarity using hierarchical clustering analysis. Each column represents one sample and each row is a single gene. Extracellular matrix (ECM, orange), Immune-related (black) and Epithelial (yellow) genes are indicated at the left side annotation bar. B. Heatmap of group average normalized expression values are shown here. with significant differences between infant (pink) and adult (blue all adults; purple 20 years; green 60 years) groups. C. Log10 values of the all-sample average expression signals were plotted for each gene. D. Negative log10 of the adjusted P-value of the Limma testing for adult vs. infant comparison was plotted for each gene. Many of the negative log10(AdjPvalue) values are over 10, indicating large differences (high significance). The z-score is displayed in the blue-white-red color gradient from -2 as the darkest blue, 0 as white, and 2 as darkest red color.
Table 2.
Selected Gene Ontology (GO) biological themes with enriched gene expression in infant skin.
Fig 3.
Results of the enrichment analysis against various databases including Gene Ontology for infant skin: Molecular Function (GO MF), Cellular component (GO CC), and Biological Process (GO BP) are shown for the terms with the lowest adjusted P-values in the infant samples.
FDR adjusted P-values were used to select significant pathways. NegLog10Qvalue indicates -Log10FDR adjusted P-value.
Fig 4.
Results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis (GeneRatio) are shown for the fifteen most significant pathways in infant skin.
FDR adjusted p-values were used to select significant pathways. Dot size represents the number of genes in each pathway (Count); p.adjust (FDR adjusted P-value) and red < purple < blue.
Fig 5.
Hierarchical clustering analysis of differentially expressed genes for ECM, LCE and MHC in full-thickness skin tissue for infants and adults.
A. Heatmap of samples showing normalized expression values (based on z-score) of selected differentially regulated genes with adjusted P value < 0.05 and absolute fold change > = 1.5 associated with ECM, LCE, and MHC for infant and adult (A20s: 20 years old, A60s: 60 years old). Euclidean distances between each sample were calculated and an unsupervised hclust algorithm was used for clustering analysis. Samples formed 2 clusters clearly separating infants (pink) and adults (blue, all adults; purple, 20 years; green, 60 years). Genes were grouped for similarity using hierarchical cluster analysis. Each column represents one sample and each row is a single gene. Infant samples have higher ECM gene expression (orange) and lower MHC (black) and LCE (yellow) expression than adult samples. B. Heatmap of group average normalized expression values is shown here with significant differences between infant (pink) and adult (blue all adults, purple 20 years; green 60 years) groups. C. Log10 values of the all-sample average expression signal were plotted for each gene. D. Negative log10 of the adjusted P value of the Limma testing for adult vs. infant comparison were plotted for each gene in the ECM, LCE and MHC classes. Many of the negative log10(AdjPvalue) values are over 10, indicating large difference (high significance). The z-score is displayed in the blue-white-red color gradient from -2 as the darkest blue, 0 as white, and 2 as darkest red color.
Table 3.
Selected Gene Ontology biological themes with enriched gene expression in adult skin.
Fig 6.
The results of the enrichment analysis against various databases including Gene Ontology for adult skin: Molecular Function (GO MF), Cellular component (GO CC), and Biological Process (GO BP) are shown for adult skin with the top most significantly increased terms.
FDR adjusted P-values were used to select significant pathways. NegLog10Qvalue indicates -Log10FDR adjusted P-value.
Fig 7.
Results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis (GeneRatio) are shown for the thirty-eight most significant pathways in adult skin.
FDR adjusted P-values were used to select significant pathways. Dot size represents the number of genes in each pathway (Count); p.adjust (FDR adjusted P value) and red < purple < blue.
Table 4.
Comparative overexpression for selected gene families for infant skin versus adult skin.