Table 3.
Selected Gene Groups Present in the Bone-Formation (Down) Clusters, Which Were Downregulated During Matrix Formation
| Gene group | Cluster | Gene name |
|---|---|---|
| Calcium signaling | ||
| Asph | H | Aspartate-β-hydroxylase |
| Cab39l | L | Calcium-binding protein 39-like |
| Calb2 | H | Calbindin 2 |
| Camk2b | H | Calcium/calmodulin-dependent protein kinase (CaM kinase) IIβ |
| Casq2 | H | Calsequestrin 2 |
| Pvalb | H | Parvalbumin |
| Stc2 | L | Stanniocalcin 2 |
| Trdn | H | Triadin |
| Cell cycle | ||
| Ccna2 | L | Cyclin A2 |
| Ccnb1 | L | Cyclin B1 |
| Cdc25b | L | Cell division cycle 25 homologue B |
| Cenpc1 | L | Centromere protein C1 |
| Chemokine | ||
| Ccl11 | L | Chemokine (C–C motif) ligand 11 |
| Ccr1 | L | Chemokine (C–C motif) receptor 1 |
| Ccr2 | L | Chemokine (C–C motif) receptor 2 |
| Ccr3 | L | Chemokine (C–C motif) receptor 3 |
| Cxcl12 | L | Chemokine (C–X–C motif) ligand 12 |
| Cxcl14 | H | Chemokine (C–X–C motif) ligand 14 |
| Cxcr5 | L | Chemokine (C–X–C motif) receptor 5 |
| Cytokine | ||
| Asb2 | H | Ankyrin repeat and SOCS box-containing 2 |
| Il8rb | L | Interleukin 8 receptor, β |
| Tnfsf10 | H | Tumor necrosis factor (ligand) superfamily, member 10 (TRAIL) |
| Tnfrsf14 | L | Tumor necrosis factor receptor superfamily, member 14 |
| Growth factor | ||
| Egf | L | Epidermal growth factor |
| Fgf1 | L | Fibroblast growth factor 1 |
| Fgf7 | H | Fibroblast growth factor 7 |
| Fgf23 | H | Fibroblast growth factor 23 |
| Fgl2 | H | Fibrinogen-like 2 |
| Hgf | L | Hepatocyte growth factor |
| Igfbp6 | L | Insulin-like growth factor–binding protein 6 |
| Ion channel | ||
| Cacnb1 | H | Calcium channel, voltage-dependent, β1 subunit |
| Cacng1 | H | Calcium channel, voltage-dependent, γ subunit 1 |
| Cacng7 | H | Calcium channel, voltage-dependent, γ subunit 7 |
| Clca2 | L | Chloride channel calcium activated 2 |
| Clic5 | L | Chloride intracellular channel 5 |
| Hcn4 | L | Hyperpolarization activated cyclic nucleotide-gated potassium channel 4 |
| Kcnj3 | L | Potassium inwardly rectifying channel, subfamily J, member 3 |
| Kcnj11 | H | Potassium inwardly rectifying channel, subfamily J, member 11 |
| Kcnj12 | H | Potassium inwardly rectifying channel, subfamily J, member 12 |
| Kcnn4 | L | Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 |
| Sclt1 | L | Sodium channel and clathrin linker 1 |
| Scn4a | H | Sodium channel, voltage-gated, type 4, α subunit |
| Scn4b | H | Sodium channel, type IV, β |
| Scn7a | L | Sodium channel, voltage-gated, type VII, α |
| Matrix | ||
| Efemp1 | H | EGF-containing fibulin-like extracellular matrix protein 1 |
| Mmp8 | L | Matrix metallopeptidase 8 |
| Prelp | L | Proline arginine–rich end leucine-rich repeat protein |
| Serpinb2 | L | Serine (or cysteine) peptidase inhibitor, clade B, member 2 |
| Spon1 | L | Spondin 1 |
| Muscle | ||
| Acta1 | H | Actin, α1 |
| Actn3 | H | Actinin, α3 |
| Ampd1 | H | Adenosine monophosphate deaminase 1 (isoform M) |
| Des | H | Desmin |
| Dmd | H | Dystrophin, muscular dystrophy |
| Gyg1 | H | Glycogenin 1 |
| Mb | H | Myoglobin |
| Myl1 | H | Myosin, light polypeptide 1 |
| Mylk2 | H | Myosin light chain kinase 2 |
| Mylpf | H | Myosin light chain, phosphorylatable, fast |
| Myocd | H | Myocardin |
| Smpx | H | Small muscle protein, X-linked |
| Synm | H | Synemin |
| Tnni2 | H | Troponin I type 2 |
| Tnnt3 | H | Troponin T type 3 |
| Tpm2 | L | Tropomyosin 2 |
| Neurotransmitter | ||
| Chrna1 | H | Cholinergic receptor, nicotinic, α1 |
| Chrnb1 | H | Cholinergic receptor, nicotinic, β1 |
| Chrne | H | Cholinergic receptor, nicotinic, ɛ |
| Htr1b | L | 5-Hydroxytryptamine (serotonin) receptor 1B |
| Maob | L | Monoamine oxidase B |
| Solute carrier | ||
| Slc2a1 | H | Solute carrier family 2 (facilitated glucose transporter), member 1 |
| Slc4a1 | L | Solute carrier family 4 (anion exchanger), member 1 |
| Slc6a4 | L | Solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 |
| Slc6a20 | L | Solute carrier family 6 (neurotransmitter transporter), member 20 |
| Slc14a1 | L | Solute carrier family 14 (urea transporter), member 1 |
| Slc15a2 | L | Solute carrier family 15 (H+/peptide transporter), member 2 |
| Slc16a1 | L | Solute carrier family 16, member 1 (monocarboxylic acid transporter 1) |
| Slc16a3 | H | Solute carrier family 16, member 3 (monocarboxylic acid transporter 4) |
| Slc16a6 | L | Solute carrier family 16, member 6 (monocarboxylic acid transporter 7) |
| Slc22a3 | H | Solute carrier family 22 (extraneuronal monoamine transporter), member 3 |
| Slc25a11 | L | Solute carrier family 25 (mitochondrial carrier, oxoglutarate carrier), member 11 |
| Slc25a30 | L | Solute carrier family 25, member 30 |
| Slc38a1 | L | Solute carrier family 38, member 1 |
| Slc38a3 | L | Solute carrier family 38, member 3 |
| Slco1a4 | H | Solute carrier organic anion transporter family, member 1a4 |
| TGF-β signaling | ||
| Bmpr1b | H | Bone morphogenetic protein receptor, type IB |
| Chrdl1 | L | Chordin-like 1 |
| Grem1 | H | Gremlin 1, cysteine knot superfamily |
| Tgfbr3 | L | Transforming growth factor, β receptor III |
| Ubiquitin | ||
| Usp1 | L | Ubiquitin-specific peptidase 1 |
| Usp15 | L | Ubiquitin-specific peptidase 15 |
| Wnt/β-catenin signaling (inhibitors) | ||
| Sfrp4 | H | Secreted frizzled-related protein 4 |
| Sost | L | Sclerosteosis |
| Other | ||
| Adrb2 | H | Adrenergic, β2, receptor, surface |
| Casp1 | L | Caspase 1 |
| Fcn1 | L | Ficolin (collagen/fibrinogen domain containing) 1 |
| Lepr | L | Leptin receptor |
| Mustn1 | L | Musculoskeletal, embryonic nuclear protein 1 |
| Ptgds2 | L | Prostaglandin D2 synthase 2, hematopoietic |
| Rsad2 | L | Radical S-adenosyl methionine domain containing 2 |
H = high-magnitude cluster; L = low-magnitude cluster.