Table 2.
Major genes which were overall differently expressed (greater than 1.5-log2 folds up and down and a raw p-value < 0.05) in PM-exposed HDFs compared to their control fibroblasts (n = 8 sample pairs, all from non-sun exposed areas, ages 9–94 years old, average 40.5) (PM/control. Log2 fc) are shown. The impact of PM on the gene expression of young (n = 4 sample pairs, ages 9–11, average 10.2) (PM/control. Log2 fc (young)) and old (n = 4 sample pairs, ages 55–94, average: 70.5) HDFs (PM/control. Log2 fc (old)) are also separately presented. Differentially expressed genes were analyzed using the estimates of abundances for each gene in samples. Genes were excluded if they had at least one zero FPKM values in the samples. To facilitate log2 transformation, 1 was added to each FPKM value of filtered genes. Filtered data were log2-transformed and submitted to quantile normalization. Statistical significance of the differential expression data was determined using independent t-test and fold change in which the null hypothesis was that there is no difference among groups. False discovery rate (FDR) was controlled by adjusting the p-value with the Benjamini–Hochberg algorithm. Log2 fc (fold change): log ratio with the logarithm to base 2 applied.
| PM/Control. Log2 fc | PM/Control. Log2 fc (Young) | PM/Control. Log2 fc (Old) | |
|---|---|---|---|
| IL-1β | 4.678166 | 8.732704 | 1.772352 |
| IL-6 | 2.593295 | 4.143132 | 1.463454 |
| IL-8 (CXCL8) | 3.634443 | 4.527864 | 2.403414 |
| IL-33 | 3.237957 | 3.337679 | 2.863740 |
| MMP-1 | 3.189445 | 2.380204 | 3.166181 |
| MMP-3 | 2.106478 | 6.295658 | 1.533143 |
| CYP1A1 (Cytochrome P450 1A1) | 4.844863 | 5.736596 | 2.106431 |
| CYP1B1 (Cytochrome P450 1B1) | 3.452584 | 2.917612 | 3.750746 |
| TGF-β | −2.772363 | −1.168725 | −2.549271 |
| COL1A1 (Collagen type I alpha 1 chain) | −2.022854 | −1.938849 | −1.915619 |
| COL1A2 (Collagen type I alpha 2 chain) | −1.800164 | −1.818843 | −1.666592 |
| ELN (Elastin) | −2.644748 | −2.094849 | −3.379390 |