Table 5.
Canonical pathways and gene ontologies enriched by differentially methylated genes with common differentially methylated CpG sites between dSSc and lSSc
| Category | ID | Term | p Value | Fold enrichment | FDR |
|---|---|---|---|---|---|
| (A) Canonical pathways | |||||
| KEGG_PATHWAY | hsa04512 | ECM–receptor interaction | 2.92E-03 | 5.95 | 0.03 |
| KEGG_PATHWAY | hsa04510 | Focal adhesion | 8.86E-03 | 3.32 | 0.09 |
| (B) Gene ontologies of hypomethylated common gens between dSSc and lSSc* | |||||
| GOTERM_BP_FAT | GO:0043407 | Negative regulation of MAP kinase activity | 2.14E-04 | 16.63 | 0.00 |
| GOTERM_BP_FAT | GO:0048858 | Cell projection morphogenesis | 9.72E-04 | 4.40 | 0.02 |
| GOTERM_BP_FAT | GO:0007409 | Axonogenesis | 1.11E-03 | 4.96 | 0.02 |
| GOTERM_BP_FAT | GO:0032990 | Cell part morphogenesis | 1.29E-03 | 4.21 | 0.02 |
| GOTERM_BP_FAT | GO:0007155 | Cell adhesion | 1.89E-03 | 2.57 | 0.03 |
| GOTERM_BP_FAT | GO:0003012 | Muscle system process | 2.71E-03 | 4.99 | 0.04 |
| GOTERM_BP_FAT | GO:0030030 | Cell projection organisation | 3.47E-03 | 3.25 | 0.05 |
| GOTERM_BP_FAT | GO:0030029 | Actin filament-based process | 3.88E-03 | 3.97 | 0.06 |
| GOTERM_BP_FAT | GO:0051674 | Localisation of cell | 3.97E-03 | 3.51 | 0.06 |
| GOTERM_BP_FAT | GO:0048870 | Cell motility | 3.97E-03 | 3.51 | 0.06 |
| GOTERM_BP_FAT | GO:0000904 | Cell morphogenesis involved in differentiation | 4.15E-03 | 3.93 | 0.06 |
| GOTERM_BP_FAT | GO:0010604 | Positive regulation of macromolecule metabolic process | 4.64E-03 | 2.24 | 0.07 |
| GOTERM_BP_FAT | GO:0042325 | Regulation of phosphorylation | 5.26E-03 | 2.83 | 0.08 |
| GOTERM_BP_FAT | GO:0006469 | Negative regulation of protein kinase activity | 5.85E-03 | 6.88 | 0.09 |
| GOTERM_BP_FAT | GO:0045893 | Positive regulation of transcription, DNA-dependent | 6.17E-03 | 2.76 | 0.09 |
| GOTERM_BP_FAT | GO:0043405 | Regulation of MAP kinase activity | 6.31E-03 | 5.09 | 0.09 |
| GOTERM_BP_FAT | GO:0051254 | Positive regulation of RNA metabolic process | 6.54E-03 | 2.74 | 0.10 |
| GOTERM_BP_FAT | GO:0033673 | Negative regulation of kinase activity | 6.59E-03 | 6.65 | 0.10 |
*
Number of hypermethylated common genes between dSSc and lSSc is inadequate to evaluate hypermethylated ontologies.
ECM, extracellular matrix; FDR, false discovery rate; GOTERM_BP_FAT, Gene Ontology term biological process; KEGG, Kyoto Encyclopedia of Genes and Genomes.