Table 2.
Gene ontology analysis of the 61 differentially expressed genes in idiopathic pulmonary fibrosis (IPF) fibroblasts treated with epigallocatechin gallate (EGCG) using the Database for Annotation, Visualization and Integrated Discovery (DAVID).
| Category and Term | Gene Count | Genes | Fold Enrichment | p-Value | Adjusted p-Value |
|---|---|---|---|---|---|
| Cellular components | |||||
| Endoplasmic reticulum | 15 | GABARAPL1, MSMO1, HMGCR, CYP51A1, SCD, FDFT1, SQSTM1, SQLE, DHCR7, INSIG1, CEMIP, PCSK9, HSD17B7, NSDHL, DHCR24 | 5.41 | 3.54 × 10−7 | 3.75 × 10−5 |
| Endoplasmic reticulum membrane | 14 | SC5D, MSMO1, CYP51A1, SQLE, HMGCR, SCD, DHCR7, INSIG1, LSS, ABCA1, HSD17B7, NSDHL, FDFT1, DHCR24 | 4.85 | 3.55 × 10−6 | 1.88 × 10−4 |
| Biological processes | |||||
| Cholesterol biosynthetic process | 15 | MSMO1, MVD, HMGCR, CYP51A1, HMGCS1, FDPS, LSS, FDFT1, SQLE, DHCR7, INSIG1, IDI1, HSD17B7, NSDHL, DHCR24 | 108.66 | 9.71 × 10−26 | 4.19 × 10−23 |
| Isoprenoid biosynthetic process | 6 | MVD, HMGCR, FDPS, HMGCS1, IDI1, FDFT1 | 117.98 | 9.59 × 10−10 | 2.07 × 10−7 |
| Oxidation-reduction process | 11 | SC5D, MSMO1, SQLE, HMGCR, CYP51A1, SCD, DHCR7, HSD17B7, NSDHL, FDFT1, DHCR24 | 5.11 | 4.23 × 10−5 | 0.0061 |
| Cholesterol biosynthetic process via lathosterol | 3 | SC5D, DHCR7, DHCR24 | 206.46 | 7.50 × 10−5 | 0.0080 |
| Cholesterol biosynthetic process via desmosterol | 3 | SC5D, DHCR7, DHCR24 | 206.46 | 7.50 × 10−5 | 0.0080 |
| Cholesterol homeostasis | 5 | TMEM97, FABP3, PCSK9, MYLIP, ABCA1 | 21.51 | 7.97 × 10−5 | 0.0068 |
| Steroid biosynthetic process | 4 | CYP51A1, LSS, NSDHL, FDFT1 | 34.41 | 0.0002 | 0.0143 |
* p-values adjusted with false discovery rate using the method by Benjamini et al. The gene predicted as the target of the significantly dysregulated microRNA (Table 1) is highlighted with bold font and underlined.