Table 1.
Significantly Enriched Pathways in Each Cluster
| Cluster 1 | p | Cluster 2 | p | Cluster 3 | p |
|---|---|---|---|---|---|
| IL-9 signaling | 0.0051 | Estrogen-mediated S-phase Entry | 0.0001 | Estrogen-dependent breast cancer signaling | 0.0100 |
| Insulin receptor signaling | 0.0085 | HIPPO signaling | 0.0002 | Reelin signaling in neurons | 0.0158 |
| Heparan sulfate biosynthesis (late stages) | 0.0107 | Dermatan sulfate biosynthesis (late stages) | 0.0010 | TR/RXR activation | 0.0182 |
| 3-Phosphoinositide biosynthesis | 0.0129 | Chondroitin sulfate biosynthesis (late stages) | 0.0012 | Glioma signaling | 0.0224 |
| Glioma invasiveness signaling | 0.0138 | Heparan sulfate biosynthesis (late stages) | 0.0017 | Neuropathic pain signaling in dorsal horn neurons | 0.0245 |
| Heparan sulfate biosynthesis | 0.0138 | Wnt/1β-catenin signaling | 0.0017 | Glucocorticoid receptor signaling | 0.0257 |
| ErbB4 signaling | 0.0151 | Chondroitin sulfate biosynthesis | 0.0022 | Hereditary breast cancer signaling | 0.0324 |
| Role of JAK1 and JAK3 in γc cytokine signaling | 0.0166 | Heparan sulfate biosynthesis | 0.0027 | Insulin receptor signaling | 0.0427 |
| Erythropoietin signaling | 0.0186 | Dermatan sulfate biosynthesis | 0.0027 | eNOS signaling | 0.0468 |
| Growth hormone signaling | 0.0200 | Cyclins and cell cycle regulation | 0.0081 | Regulation of eIF4 and 70S6K Signaling | 0.0490 |
| ERK/MAPK signaling | 0.0209 | Isoleucine degradation 1 | 0.0087 | ||
| JAK/Stat signaling | 0.0214 | D-myoinositol (1,4,5,6)- tetrakisphosphate biosynthesis | 0.0095 | ||
| Prolactin signaling | 0.0219 | D-myoinositol (3,4,5,6)- tetrakisphosphate biosynthesis | 0.0095 | ||
| Superpathway of inositol phosphate compounds | 0.0224 | Cell cycle: G2/M DNA damage checkpoint regulation | 0.0135 | ||
| HIPPO signaling | 0.0302 | Breast cancer regulation by Stathmin1 | 0.0135 | ||
| IGF-l signaling | 0.0372 | Superpathway of inositol phosphate compounds | 0.0138 | ||
| Amyotrophic lateral sclerosis signaling | 0.0380 | GADD45 signaling | 0.0155 | ||
| p53 signaling | 0.0380 | DNA damage-induced 14-3-30 signaling | 0.0155 | ||
| Telomerase signaling | 0.0389 | D-myo-inositol-5-phosphate metabolism | 0.0155 | ||
| Neuropathic pain signaling in dorsal horn neurons | 0.0389 | 3-Phosphoinositide degradation | 0.0158 | ||
| HIF1α signaling | 0.0407 | Glioblastoma multiforme signaling | 0.0166 | ||
| HGF signaling | 0.0427 | Unfolded protein response | 0.0174 | ||
| Pancreatic adenocarcinoma signaling | 0.0437 | Role of CHK proteins in cell cycle checkpoint control | 0.0182 | ||
| Regulation of cellular mechanics by calpain protease | 0.0204 | ||||
| 3-Phosphoinositide biosynthesis | 0.0209 | ||||
| ATM signaling | 0.0219 | ||||
| cAMP-mediated signaling | 0.0245 | ||||
| Cell cycle: Gl/S checkpoint regulation | 0.0275 | ||||
| Antiproliferative role of TOB in T cell signaling | 0.0282 | ||||
| Synaptic long-term potentiation | 0.0331 | ||||
| Caveolar-mediated endocytosis signaling | 0.0372 | ||||
| STAT3 pathway | 0.0380 | ||||
| ERK/MAPK signaling | 0.0427 | ||||
| G-protein coupled receptor signaling | 0.0468 | ||||
| Insulin receptor signaling | 0.0479 | ||||
| Cell cycle regulation by BTG family proteins | 0.0490 | ||||
| Role of JAK2 in hormone-like cytokine signaling | 0.0490 |
Target genes of miRNAs in each cluster (Fig. 2B) are identified by Target Scan. To find enriched pathways, each gene group is analyzed by Ingenuity Pathway Analysis. A few examples of the spectrum of pathways that can effect cell proliferation, cartilage and bone are bolded.