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.