Table 2.
Selected Gene Groups Present in the Bone-Formation (Up) Clusters, Which Were Upregulated During Matrix Formation
| Gene group | Cluster | Gene name |
|---|---|---|
| Apoptosis | ||
| Aifm3 | L | Apoptosis-inducing factor, mitochondrion-associated 3 |
| Bok | L | BCL2-related ovarian killer |
| Dad1 | L | Defender against cell death 1 |
| Calcium signaling | ||
| Atp2b2 | L | ATPase, Ca2+ transporting, plasma membrane 2 |
| Cacnb3 | M | Calcium channel, voltage-dependent, β3 subunit |
| Cadps | M | Ca2+-dependent secretion activator |
| Calu | M | Calumenin |
| Capn6 | M | Calpain 6 |
| Flvcr2 | L | Feline leukemia virus subgroup C cellular receptor family, member 2 |
| Hpcal1 | L | Hippocalcin-like 1 |
| Stc1 | L | Stanniocalcin 1 |
| Syt3 | L | Synaptotagmin III |
| Cytokine | ||
| Il4 | L | Interleukin 4 |
| Il11 | L | Interleukin 11 |
| Il12a | M | Interleukin 12a |
| Socs2 | L | Suppressor of cytokine signaling 2 |
| Growth factor | ||
| Fgf14 | L | Fibroblast growth factor 14 |
| Pdgfa | L | Platelet-derived growth factor α polypeptide |
| Pdgfc | M | Platelet-derived growth factor C |
| Pdgfrl | M | Platelet-derived growth factor receptor–like |
| Pgf | L | Placental growth factor |
| Ion channel | ||
| Kcne3 | M | Potassium voltage-gated channel, Isk-related subfamily, gene 3 |
| Kcng3 | L | Potassium voltage-gated channel, subfamily G, member 3 |
| Kcnk6 | M | Potassium inwardly rectifying channel, subfamily K, member 6 |
| Kcnma1 | M | Potassium large conductance calcium-activated channel, subfamily M, α member 1 |
| Kcnn2 | M | Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2 |
| Kcns1 | L | Potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1 |
| Scn1a | L | Sodium channel, voltage-gated, type I, α |
| Matrix | ||
| Acan | H | Aggrecan |
| Alpl | M | Alkaline phosphatase, liver/bone/kidney |
| Bglap | M | Bone γ-carboxyglutamate (gla) protein (osteocalcin) |
| Bgn | M | Biglycan |
| Col1a2 | M | Collagen, type I, α2 |
| Col2a1 | M | Collagen, type II, α1 |
| Col3a1 | M | Collagen, type III, α1 |
| Col5a1 | H | Collagen, type V, α1 |
| Col11a2 | H | Collagen, type XI, α2 |
| Col16a1 | M | Collagen, type XVI, α1 |
| Cthrc1 | H | Collagen triple-helix-repeat-containing 1 |
| Efemp2 | L | EGF-containing fibulin-like extracellular matrix protein 2 |
| Fn1 | M | Fibronectin 1 |
| Ibsp | M | Integrin-binding sialoprotein |
| Lepre1 | H | Leucine proline–enriched proteoglycan (leprecan) 1 |
| Lox | H | Lysyl oxidase |
| Mmp2 | M | Matrix metallopeptidase 2 |
| Mmp9 | M | Matrix metallopeptidase 9 |
| Mmp14 | M | Matrix metallopeptidase 14 |
| Mmp16 | M | Matrix metallopeptidase 16 |
| Mmp23 | M | Matrix metallopeptidase 23 |
| Omd | M | Osteomodulin |
| P4ha1 | M | Procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), α polypeptide I |
| P4ha3 | M | Procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), α polypeptide III |
| P4hb | M | Prolyl 4-hydroxylase, β polypeptide |
| Pcolce | M | Procollagen C-endopeptidase enhancer |
| Plod2 | M | Procollagen lysine, 2-oxoglutarate 5-dioxygenase 2 |
| Plod3 | M | Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 |
| Sparc | L | Secreted protein, acidic, cysteine-rich (osteonectin) |
| Timp1 | H | TIMP metallopeptidase inhibitor 1 |
| Vcan | H | Versican |
| Muscle | ||
| Myo1b | M | Myosin Ib |
| Myo5a | M | Myosin Va |
| Tpm4 | L | Tropomyosin 4 |
| Tuba3a | L | Tubulin, α3A |
| Neurotransmitter | ||
| Drd1a | L | Dopamine receptor D1A |
| Glrb | L | Glycine receptor, β |
| Htr1d | L | 5-Hydroxytryptamine (serotonin) receptor 1D |
| Htr2a | M | 5-hydroxytryptamine (serotonin) receptor 2A |
| Syn1 | L | synapsin I |
| Solute Carrier | ||
| Slc1a4 | L | solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 |
| Slc2a13 | M | solute carrier family 2 (facilitated glucose transporter), member 13 |
| Slc5a5 | L | solute carrier family 5 (sodium iodide symporter), member 5 |
| Slc6a2 | M | Solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2 |
| Slc6a15 | M | Solute carrier family 6 (neutral amino acid transporter), member 15 |
| Slc7a8 | L | Solute carrier family 7 (cationic amino acid transporter, y+ system), member 8 |
| Slc8a3 | M | Solute carrier family 8 (sodium/calcium exchanger), member 3 |
| Slc9a2 | H | Solute carrier family 9 (sodium/hydrogen exchanger), member 2 |
| Slc9a4 | M | Solute carrier family 9 (sodium/hydrogen exchanger), member 4 |
| Slc13a5 | H | Solute carrier family 13 (sodium-dependent citrate transporter), member 5 |
| Slc25a1 | L | Solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1 |
| Slc26a2 | L | Solute carrier family 26 (sulfate transporter), member 2 |
| Slc30a4 | M | Solute carrier family 30 (zinc transporter), member 4 |
| Slc31a1 | M | Solute carrier family 31 (copper transporters), member 1 |
| Slc35b1 | L | Solute carrier family 35, member B1 |
| Slc36a1 | M | Solute carrier family 36 (proton/amino acid symporter), member 1 |
| Slc36a2 | H | Solute carrier family 36 (proton/amino acid symporter), member 2 |
| Slc39a7 | M | Solute carrier family 39 (zinc transporter), member 7 |
| Slc39a8 | M | Solute carrier family 39 (metal ion transporter), member 8 |
| Slco3a1 | L | Solute carrier organic anion transporter family, member 3a1 |
| TGF-β signaling | ||
| Bambi | M | BMP and activin membrane–bound inhibitor |
| Bmp2 | L | Bone morphogenetic protein 2 |
| Hnf4a | L | Hepatocyte nuclear factor 4, α |
| Inhba | L | Inhibin β-A |
| Nkx2-5 | L | NK2 transcription factor related, locus 5 |
| Smad9 | M | SMAD family member 9 |
| Tgfb1 | L | Transforming growth factor, β1 |
| Tgfb3 | L | Transforming growth factor, β3 |
| Vdr | L | Vitamin D (1,25-dihydroxyvitamin D3) receptor |
| Wnt/β-catenin signaling | ||
| Cdh2 | M | Cadherin 2 |
| Cpz | H | Carboxypeptidase Z |
| Gja1 | M | Gap junction protein, α1 |
| Kremen1 | M | Kringle-containing transmembrane protein 1 |
| Wif1 | M | Wnt inhibitory factor 1 |
| Wisp1 | M | Wnt1 inducible signaling pathway protein 1 |
| Other | ||
| Ccnd1 | M | Cyclin D1 |
| Creb3l1 | H | cAMP-responsive element–binding protein 3-like 1 |
| Foxs1 | L | Forkhead box S1 |
| Hif1a | L | Hypoxia-inducible factor 1, α subunit |
| Jund | L | Jun D protooncogene |
| Pthr1 | M | Parathyroid hormone receptor 1 |
| Sox11 | L | SRY (sex-determining region Y)-box 11 |
| Sp7 | M | Sp7 transcription factor (osterix) |
H = high-magnitude cluster; M = medium-magnitude cluster; L = low-magnitude cluster.