Table 4.
Functional clustering of differentially expressed genes (1595 annotated) with Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7
| Category | Term | Count | % | Fold enrichment | P‐value | FDR |
|---|---|---|---|---|---|---|
| Annotation Cluster 1 Enrichment Score: 3.46 | ||||||
| GOTERM_MF_FAT | GO:0046983–protein dimerization activity | 75 | 4.70 | 1.6 | 3.81E − 05 | 6.10E − 02 |
| GOTERM_MF_FAT | GO:0042802–identical protein binding | 82 | 5.14 | 1.5 | 2.27E − 04 | 3.63E − 01 |
| GOTERM_MF_FAT | GO:0042803–protein homodimerization activity | 44 | 2.76 | 1.5 | 4.66E − 03 | 7.21E + 00 |
| Annotation Cluster 2 Enrichment Score: 3.36 | ||||||
| GOTERM_CC_FAT | GO:0043232–intracellular non‐membrane‐bounded organelle | 294 | 18.43 | 1.3 | 1.69E − 06 | 2.47E − 03 |
| GOTERM_CC_FAT | GO:0043228–non‐membrane‐bounded organelle | 294 | 18.43 | 1.3 | 1.69E − 06 | 2.47E − 03 |
| GOTERM_MF_FAT | GO:0003779–actin binding | 53 | 3.32 | 1.9 | 8.73E − 06 | 1.40E − 02 |
| SP_PIR_KEYWORDS | Actin binding | 41 | 2.57 | 2.1 | 1.84E − 05 | 2.76E − 02 |
| GOTERM_CC_FAT | GO:0015629–actin cytoskeleton | 45 | 2.82 | 1.9 | 5.17E − 05 | 7.54E − 02 |
| SP_PIR_KEYWORDS | Cytoskeleton | 80 | 5.02 | 1.6 | 8.37E − 05 | 1.25E − 01 |
| GOTERM_MF_FAT | GO:0008092–cytoskeletal protein binding | 69 | 4.33 | 1.6 | 1.10E – 04 | 1.77E − 01 |
| GOTERM_BP_FAT | GO:0030036–actin cytoskeleton organization | 36 | 2.26 | 1.8 | 6.89E − 04 | 1.25E + 00 |
| GOTERM_CC_FAT | GO:0005856–cytoskeleton | 156 | 9.78 | 1.3 | 9.63E − 04 | 1.40E + 00 |
| GOTERM_BP_FAT | GO:0030029–actin filament‐based process | 37 | 2.32 | 1.7 | 1.14E − 03 | 2.07E + 00 |
| GOTERM_BP_FAT | GO:0007010–cytoskeleton organization | 57 | 3.57 | 1.5 | 2.50E − 03 | 4.48E + 00 |
| GOTERM_CC_FAT | GO:0015630–microtubule cytoskeleton | 62 | 3.89 | 1.3 | 3.99E − 02 | 4.48E + 01 |
| GOTERM_CC_FAT | GO:0005815–microtubule organizing center | 32 | 2.01 | 1.4 | 4.14E − 02 | 4.61E + 01 |
| GOTERM_CC_FAT | GO:0005813–centrosome | 28 | 1.76 | 1.4 | 6.38E − 02 | 6.18E + 01 |
| GOTERM_CC_FAT | GO:0044430–cytoskeletal part | 98 | 6.14 | 1.2 | 8.30E − 02 | 7.17E + 01 |
| Annotation Cluster 3 Enrichment Score: 3.29 | ||||||
| GOTERM_BP_FAT | GO:0007155–cell adhesion | 94 | 5.89 | 1.5 | 3.12E − 05 | 5.72E − 02 |
| GOTERM_BP_FAT | GO:0022610–biological adhesion | 94 | 5.89 | 1.5 | 3.30E – 05 | 6.04E − 02 |
| SP_PIR_KEYWORDS | Cell adhesion | 55 | 3.45 | 1.6 | 5.24E − 04 | 7.83E − 01 |
| GOTERM_BP_FAT | GO:0016337–cell‐cell adhesion | 31 | 1.94 | 1.3 | 1.32E − 01 | 9.26E + 01 |
| Annotation Cluster 4 Enrichment Score: 3.14 | ||||||
| SP_PIR_KEYWORDS | ECM | 55 | 3.45 | 2.8 | 4.16E − 12 | 6.24E − 09 |
| GOTERM_CC_FAT | GO:0031012–ECM | 70 | 4.39 | 2.3 | 8.15E − 11 | 1.19E − 07 |
| GOTERM_CC_FAT | GO:0005578–proteinaceous ECM | 65 | 4.08 | 2.3 | 4.01E − 10 | 5.85E − 07 |
| GOTERM_CC_FAT | GO:0005581–collagen | 16 | 1.00 | 5.1 | 9.18E − 08 | 1.34E − 04 |
| GOTERM_CC_FAT | GO:0044420–ECM part | 30 | 1.88 | 2.9 | 2.59E − 07 | 3.78E − 04 |
| SP_PIR_KEYWORDS | Hydroxylation | 21 | 1.32 | 3.7 | 5.20E − 07 | 7.79E − 04 |
| SP_PIR_KEYWORDS | Triple helix | 13 | 0.82 | 5.2 | 2.48E − 06 | 3.72E − 03 |
| SP_PIR_KEYWORDS | Hydroxylysine | 12 | 0.75 | 4.8 | 1.74E − 05 | 2.60E − 02 |
| SP_PIR_KEYWORDS | Trimer | 11 | 0.69 | 5.2 | 1.85E − 05 | 2.78E − 02 |
| GOTERM_BP_FAT | GO:0030198–ECM organization | 24 | 1.50 | 2.6 | 2.79E − 05 | 5.11E − 02 |
| SP_PIR_KEYWORDS | Collagen | 21 | 1.32 | 2.7 | 6.04E − 05 | 9.05E − 02 |
| SP_PIR_KEYWORDS | Hydroxyproline | 12 | 0.75 | 4.0 | 1.11E − 04 | 1.67E − 01 |
| GOTERM_BP_FAT | GO:0043062–extracellular structure organization | 30 | 1.88 | 2.1 | 1.89E − 04 | 3.45E − 01 |
| GOTERM_CC_FAT | GO:0005583–fibrillar collagen | 7 | 0.44 | 6.6 | 2.81E − 04 | 4.09E − 01 |
| GOTERM_CC_FAT | GO:0005604–basement membrane | 18 | 1.13 | 2.6 | 4.06E − 04 | 5.91E − 01 |
| KEGG_PATHWAY | hsa04512: ECM–receptor interaction | 20 | 1.25 | 2.4 | 4.49E − 04 | 5.49E − 01 |
| INTERPRO | IPR008160: collagen triple helix repeat | 18 | 1.13 | 2.5 | 5.57E − 04 | 9.46E − 01 |
| GOTERM_BP_FAT | GO:0030199–collagen fibril organization | 10 | 0.63 | 3.9 | 6.06E − 04 | 1.10E + 00 |
| SP_PIR_KEYWORDS | Ehlers–Danlos syndrome | 6 | 0.38 | 6.7 | 1.05E − 03 | 1.56E + 00 |
| UP_SEQ_FEATURE | Domain: fibrillar collagen NC1 | 6 | 0.38 | 6.7 | 1.08E − 03 | 1.97E + 00 |
| INTERPRO | IPR000885: fibrillar collagen, C‐terminal | 6 | 0.38 | 6.5 | 1.27E − 03 | 2.14E + 00 |
| GOTERM_MF_FAT | GO:0048407–PDGF binding | 6 | 0.38 | 6.3 | 1.38E − 03 | 2.18E + 00 |
| SMART | SM00038: COLFI | 6 | 0.38 | 6.0 | 1.73E − 03 | 2.31E + 00 |
| UP_SEQ_FEATURE | Domain:TSP N‐terminal | 8 | 0.50 | 4.3 | 1.78E − 03 | 3.24E + 00 |
| UP_SEQ_FEATURE | Region of interest:triple‐helical region | 8 | 0.50 | 4.3 | 1.78E − 03 | 3.24E + 00 |
| UP_SEQ_FEATURE | Propeptide:C‐terminal propeptide | 5 | 0.31 | 7.7 | 2.34E − 03 | 4.24E + 00 |
| GOTERM_MF_FAT | GO:0005201–ECM structural constituent | 17 | 1.07 | 2.3 | 2.43E − 03 | 3.82E + 00 |
| INTERPRO | IPR003129:Laminin G, TSP‐type, N‐terminal | 7 | 0.44 | 3.8 | 8.17E − 03 | 1.31E + 01 |
| SMART | SM00210:TSPN | 7 | 0.44 | 3.5 | 1.13E − 02 | 1.42E + 01 |
| GOTERM_MF_FAT | GO:0046332–SMAD binding | 10 | 0.63 | 2.5 | 1.49E − 02 | 2.14E + 01 |
| UP_SEQ_FEATURE | Region of interest: non‐helical region | 4 | 0.25 | 6.1 | 2.20E − 02 | 3.38E + 01 |
| GOTERM_CC_FAT | GO:0005588–collagen Type V | 3 | 0.19 | 11.2 | 2.23E − 02 | 2.80E + 01 |
| SP_PIR_KEYWORDS | Pyroglutamic acid | 9 | 0.56 | 2.4 | 2.97E − 02 | 3.64E + 01 |
| UP_SEQ_FEATURE | Glycosylation site: O‐linked (Gal…) | 4 | 0.25 | 5.5 | 3.11E − 02 | 4.42E + 01 |
| GOTERM_BP_FAT | GO:0043588–skin development | 7 | 0.44 | 2.7 | 3.75E − 02 | 5.04E + 01 |
| PIR_SUPERFAMILY | PIRSF002257: collagen α1 (V) chain | 3 | 0.19 | 8.5 | 4.08E − 02 | 4.65E + 01 |
| PIR_SUPERFAMILY | PIRSF002255: collagen α1 (I) chain | 3 | 0.19 | 6.8 | 6.41E − 02 | 6.30E + 01 |
| UP_SEQ_FEATURE | Propeptide: N‐terminal propeptide | 3 | 0.19 | 6.1 | 7.96E − 02 | 7.84E + 01 |
| PIR_SUPERFAMILY | PIRSF002258:collagen α1 (IV) chain | 3 | 0.19 | 4.9 | 1.20E − 01 | 8.53E + 01 |
| GOTERM_CC_FAT | GO:0030934–anchoring collagen | 3 | 0.19 | 3.7 | 1.87E − 01 | 9.52E + 01 |
| INTERPRO | IPR012680: Laminin G, subdomain 2 | 5 | 0.31 | 1.4 | 4.78E − 01 | 1.00E + 02 |
| INTERPRO | IPR001791: Laminin G | 5 | 0.31 | 1.3 | 5.33E − 01 | 1.00E + 02 |
| SMART | SM00282: LamG | 5 | 0.31 | 1.2 | 5.89E − 01 | 1.00E + 02 |
| INTERPRO | IPR013320: Concanavalin A‐like lectin/glucanase, subgroup | 7 | 0.44 | 1.1 | 6.40E − 01 | 1.00E + 02 |
| GOTERM_BP_FAT | GO:0008544–epidermis development | 15 | 0.94 | 0.9 | 7.54E − 01 | 1.00E + 02 |
| GOTERM_BP_FAT | GO:0007398–ectoderm development | 16 | 1.00 | 0.9 | 7.71E − 01 | 1.00E + 02 |
| Annotation Cluster 5 Enrichment Score: 3.00 | ||||||
| GOTERM_CC_FAT | GO:0060205–cytoplasmic membrane‐bounded vesicle lumen | 16 | 1.00 | 4.1 | 3.02E − 06 | 4.40E − 03 |
| GOTERM_CC_FAT | GO:0031983–vesicle lumen | 16 | 1.00 | 3.9 | 5.66E − 06 | 8.26E − 03 |
| GOTERM_CC_FAT | GO:0031093–platelet α granule lumen | 15 | 0.94 | 4.1 | 6.30E − 06 | 9.20E − 03 |
| GOTERM_CC_FAT | GO:0031091–platelet α granule | 17 | 1.07 | 3.4 | 1.86E − 05 | 2.71E − 02 |
| GOTERM_CC_FAT | GO:0044433–cytoplasmic vesicle part | 30 | 1.88 | 1.8 | 2.16E − 03 | 3.11E + 00 |
| GOTERM_CC_FAT | GO:0031410–cytoplasmic vesicle | 79 | 4.95 | 1.4 | 2.61E − 03 | 3.73E + 00 |
| GOTERM_CC_FAT | GO:0016023–cytoplasmic membrane‐bounded vesicle | 69 | 4.33 | 1.4 | 3.20E − 03 | 4.57E + 00 |
| SP_PIR_KEYWORDS | Mitogen | 10 | 0.63 | 3.2 | 3.32E − 03 | 4.86E + 00 |
| GOTERM_CC_FAT | GO:0031988–membrane‐bounded vesicle | 70 | 4.39 | 1.4 | 4.51E − 03 | 6.39E + 00 |
| GOTERM_CC_FAT | GO:0031982–vesicle | 80 | 5.02 | 1.3 | 5.29E − 03 | 7.45E + 00 |
| GOTERM_CC_FAT | GO:0042470–melanosome | 16 | 1.00 | 2.0 | 1.14E − 02 | 1.54E + 01 |
| GOTERM_CC_FAT | GO:0048770–pigment granule | 16 | 1.00 | 2.0 | 1.14E − 02 | 1.54E + 01 |
| GOTERM_CC_FAT | GO:0030141–secretory granule | 26 | 1.63 | 1.6 | 1.66E − 02 | 2.17E + 01 |
| SP_PIR_KEYWORDS | Cytoplasmic vesicle | 25 | 1.57 | 1.3 | 1.55E − 01 | 9.19E + 01 |
| Annotation Cluster 6 Enrichment Score: 2.64 | ||||||
| GOTERM_BP_FAT | GO:0030334–regulation of cell migration | 35 | 2.19 | 2.4 | 3.65E − 06 | 6.69E − 03 |
| GOTERM_BP_FAT | GO:0006928–cell motion | 72 | 4.51 | 1.7 | 5.81E − 06 | 1.06E − 02 |
| GOTERM_BP_FAT | GO:0040012–regulation of locomotion | 36 | 2.26 | 2.1 | 2.53E − 05 | 4.64E − 02 |
| GOTERM_BP_FAT | GO:0051270–regulation of cell motion | 36 | 2.26 | 2.1 | 2.84E − 05 | 5.20E − 02 |
| GOTERM_BP_FAT | GO:0001944–vasculature development | 43 | 2.70 | 1.9 | 3.54E − 05 | 6.47E − 02 |
| GOTERM_BP_FAT | GO:0001568–blood vessel development | 42 | 2.63 | 1.9 | 4.35E − 05 | 7.97E − 02 |
| GOTERM_BP_FAT | GO:0032101–regulation of response to external stimulus | 27 | 1.69 | 1.9 | 1.46E − 03 | 2.63E + 00 |
| GOTERM_BP_FAT | GO:0030335–positive regulation of cell migration | 18 | 1.13 | 2.3 | 1.74E − 03 | 3.13E + 00 |
| GOTERM_BP_FAT | GO:0040017–positive regulation of locomotion | 19 | 1.19 | 2.2 | 2.04E − 03 | 3.68E + 00 |
| GOTERM_BP_FAT | GO:0016477–cell migration | 40 | 2.51 | 1.6 | 2.08E − 03 | 3.74E + 00 |
| GOTERM_BP_FAT | GO:0001525–angiogenesis | 25 | 1.57 | 1.9 | 2.44E − 03 | 4.37E + 00 |
| GOTERM_BP_FAT | GO:0051272–positive regulation of cell motion | 18 | 1.13 | 2.1 | 4.95E − 03 | 8.69E + 00 |
| GOTERM_BP_FAT | GO:0048514–blood vessel morphogenesis | 31 | 1.94 | 1.7 | 5.86E − 03 | 1.02E + 01 |
| GOTERM_BP_FAT | GO:0051674–localization of cell | 41 | 2.57 | 1.5 | 7.62E − 03 | 1.31E + 01 |
| GOTERM_BP_FAT | GO:0048870–cell motility | 41 | 2.57 | 1.5 | 7.62E − 03 | 1.31E + 01 |
| GOTERM_BP_FAT | GO:0050921–positive regulation of chemotaxis | 8 | 0.50 | 3.1 | 1.11E − 02 | 1.86E + 01 |
| GOTERM_BP_FAT | GO:0050920–regulation of chemotaxis | 8 | 0.50 | 2.9 | 1.61E − 02 | 2.57E + 01 |
| GOTERM_BP_FAT | GO:0050927–positive regulation of positive chemotaxis | 6 | 0.38 | 3.6 | 2.14E − 02 | 3.27E + 01 |
| GOTERM_BP_FAT | GO:0050926–regulation of positive chemotaxis | 6 | 0.38 | 3.6 | 2.14E − 02 | 3.27E + 01 |
| GOTERM_BP_FAT | GO:0007169–transmembrane receptor protein tyrosine kinase signaling pathway | 30 | 1.88 | 1.5 | 2.25E − 02 | 3.41E + 01 |
| GOTERM_BP_FAT | GO:0032103–positive regulation of response to external stimulus | 12 | 0.75 | 2.1 | 2.28E − 02 | 3.44E + 01 |
| GOTERM_BP_FAT | GO:0048520–positive regulation of behavior | 8 | 0.50 | 2.7 | 2.62E − 02 | 3.85E + 01 |
| GOTERM_BP_FAT | GO:0008284–positive regulation of cell proliferation | 47 | 2.95 | 1.3 | 5.82E − 02 | 6.66E + 01 |
| GOTERM_BP_FAT | GO:0050795–regulation of behavior | 8 | 0.50 | 2.0 | 1.05E − 01 | 8.70E + 01 |
| GOTERM_BP_FAT | GO:0048584–positive regulation of response to stimulus | 27 | 1.69 | 1.3 | 1.37E − 01 | 9.32E + 01 |
COLFI, fibrillar collagens C‐terminal domain; ECM, extracellular matrix; FDR, false discovery rate; LamG, Laminin G domain; PDGF, platelet‐derived growth factor; TSP, thrombospondin; TSPN, TSPN‐terminal domain.