Extended Table 2. KEGG pathway analysis of differentially expressed genes from cardiac cultures plated on soft or stiff PDMS substrates.
Global gene expression data from RNAseq analysis was used to screen for pathways with enriched differential gene expression (p<0.2, FPKM>1) using the KEGG database via DAVID. Listed are pathway terms involved in signal transduction cascades, the number of differentially expressed genes, the percentage of differentially expressed genes compared to the total number of genes associated with that pathway as well as p-values and corrected p-value Benjamini-scores obtained via the Benjamini-Hochberg procedure.
| Term | Genes# | % total | p-value | Benjamini |
|---|---|---|---|---|
| Signaling pathways regulating pluripotency of stem cells | 29 | 1.2 | 0.0002 | 0.0650 |
| Rap1 signaling pathway | 35 | 1.4 | 0.0050 | 0.2100 |
| Toll-like receptor signaling pathway | 20 | 0.8 | 0.0055 | 0.1800 |
| TNF signaling pathway | 20 | 0.8 | 0.0120 | 0.3000 |
| MAPK signaling pathway | 37 | 1.5 | 0.0210 | 0.2800 |
| PI3K-Akt signaling pathway | 48 | 2 | 0.0270 | 0.3200 |
| Adrenergic signaling in cardiomyocytes | 24 | 1 | 0.0280 | 0.3100 |
| HIF-1 signaling pathway | 18 | 0.7 | 0.0310 | 0.3300 |
| Cholinergic synapse | 19 | 0.8 | 0.0340 | 0.3500 |
| cGMP-PKG signaling pathway | 26 | 1.1 | 0.0370 | 0.3300 |
| Insulin resistance | 18 | 0.7 | 0.0500 | 0.3600 |
| AMPK signaling pathway | 20 | 0.8 | 0.0520 | 0.3700 |
| ErbB signaling pathway | 15 | 0.6 | 0.0530 | 0.3700 |
| ECM-receptor interaction | 15 | 0.6 | 0.0580 | 0.3700 |
| Neurotrophin signaling pathway | 19 | 0.8 | 0.0650 | 0.3800 |
| Estrogen signaling pathway | 16 | 0.7 | 0.0670 | 0.3800 |
| Wnt signaling pathway | 21 | 0.9 | 0.0750 | 0.4000 |
| VEGF signaling pathway | 11 | 0.4 | 0.0770 | 0.4000 |
| Hippo signaling pathway | 22 | 0.9 | 0.0820 | 0.4100 |
| Jak-STAT signaling pathway | 21 | 0.9 | 0.0930 | 0.4300 |
| Calcium signaling pathway | 25 | 1 | 0.0960 | 0.4300 |