Table 1.
Top regulated genes involved in protein degradation and muscle function in casting and tenotomy-induced muscle atrophy
| Casting Fold Change |
Tenotomy Fold Change |
||||||||
|---|---|---|---|---|---|---|---|---|---|
| Gene Name | Gene Description | Casting P Value | Tenotomy P Value | 3 Days | 7 Days | 14 Days | 3 Days | 7 Days | 14 Days |
| Collagen Metabolism | |||||||||
| Mmp2 | matrix metalloproteinase 2 | 3.1E-06 | 9.0E-14 | 1.5 | 1.1 | 1.4 | 2.6 | 4.7 | 6.2 |
| Mmp14 | matrix metallopeptidase 14 | 9.3E-04 | 6.7E-13 | 1.2 | 1.0 | 1.6 | 3.1 | 7.3 | 7.9 |
| Mmp3 | matrix metalloproteinase 3 | 2.4E-02 | 1.4E-10 | 0.6 | 1.3 | 3.7 | 2.5 | 18.0 | 6.1 |
| Mmp11 | matrix metalloproteinase 11 | 3.0E-02 | 1.3E-06 | 2.2 | 1.3 | 1.1 | 2.8 | 2.0 | 2.1 |
| Adamts2 | a disintegrin-like and metalloprotease type 2 | 3.9E-02 | 2.5E-09 | 1.1 | 1.0 | 1.3 | 1.7 | 2.4 | 2.0 |
| Mmp13 | matrix metalloproteinase 13 | 4.4E-01 | 8.0E-14 | 0.6 | 1.8 | 2.5 | 8.4 | 1217 | 406.6 |
| Caspase Activity | |||||||||
| Casp8 | caspase 8 | 5.4E-02 | 6.3E-10 | 0.9 | 1.1 | 1.5 | 2.9 | 1.7 | 1.7 |
| Casp6 | caspase 6 | 2.3E-02 | 2.0E-05 | 1.0 | 1.0 | 1.4 | 2.6 | 1.8 | 1.4 |
| Casp3 | caspase 3 | 1.5E-02 | 3.0E-10 | 1.0 | 1.4 | 1.2 | 3.3 | 2.1 | 1.8 |
| Casp11 | caspase 11 | 6.3E-01 | 1.1E-08 | 0.6 | 1.2 | 1.5 | 2.6 | 2.3 | 1.9 |
| Casp1 | caspase 1 | 1.1E-01 | 1.4E-05 | 0.9 | 1.2 | 1.4 | 7.6 | 2.2 | 1.9 |
| Apaf1 | apoptotic protease activating factor 1 | 3.8E-01 | 1.7E-09 | 0.9 | 1.0 | 1.2 | 2.5 | 1.8 | 1.3 |
| Mitochodrial Function | |||||||||
| Abcb6 | ATP-binding cassette, sub-family B, 6 | 1.2E-01 | 2.8E-07 | 1.0 | 0.9 | 0.9 | 1.0 | 0.6 | 0.7 |
| Acaa2 | mitochondrial 3-oxoacyl-Coenzyme A thiolase | 8.4E-08 | 1.4E-06 | 1.0 | 0.6 | 0.6 | 0.6 | 0.6 | 0.6 |
| Acas2l | acetyl-Coenzyme A synthetase 2 like | 6.0E-07 | 1.7E-01 | 0.6 | 0.6 | 0.8 | 1.1 | 1.2 | 1.1 |
| Bckdhb | branched chain ketoacid dehydrogenase E1 | 6.6E-01 | 1.6E-06 | 1.1 | 1.2 | 0.8 | 0.6 | 0.9 | 0.8 |
| Cox6a1 | cytochrome c oxidase, subunit VI a1 | 1.6E-01 | 9.6E-10 | 0.8 | 1.0 | 1.1 | 2.1 | 1.5 | 1.6 |
| Dlat | dihydrolipoamide S-acetyltransferase | 4.9E-08 | 7.8E-12 | 1.0 | 0.7 | 0.8 | 0.5 | 0.6 | 0.6 |
| Mrpl17 | mitochondrial ribosomal L17 | 2.3E-09 | 2.6E-04 | 0.6 | 0.8 | 0.6 | 0.7 | 0.7 | 0.7 |
| Mrpl51 | mitochondrial ribosomal L51 | 1.9E-12 | 4.0E-07 | 0.6 | 0.7 | 0.7 | 0.5 | 0.6 | 0.8 |
| Ndufab1 | NADH dehydrogenase | 1.1E-05 | 3.2E-06 | 0.7 | 0.6 | 0.8 | 0.6 | 0.5 | 0.7 |
| Ndufs4 | NADH dehydrogenase 4 | 1.6E-01 | 5.5E-07 | 1.3 | 0.8 | 0.8 | 0.6 | 0.6 | 0.7 |
| Timm22 | translocase of inner mitochondrial membrane 2 | 2.3E-03 | 9.5E-05 | 0.9 | 0.8 | 0.7 | 0.6 | 0.6 | 0.8 |
| Timm8a | translocase of inner mitochondrial membrane 8 | 3.1E-10 | 2.2E-01 | 0.6 | 0.8 | 0.9 | 1.0 | 0.9 | 0.9 |
| Muscle Biogenesis | |||||||||
| Acta2 | actin, alpha 2 | 2.6E-05 | 6.6E-02 | 1.4 | 1.5 | 1.2 | 0.6 | 0.9 | 1.0 |
| Actc1 | actin, alpha, cardiac | 5.9E-07 | 1.8E-08 | 1.1 | 0.2 | 0.5 | 0.4 | 0.2 | 0.7 |
| Actg1 | actin, gamma, cytoplasmic 1 | 3.6E-05 | 1.0E-11 | 0.6 | 0.9 | 1.1 | 2.2 | 1.5 | 1.8 |
| Dmd | dystrophin, muscular dystrophy | 7.4E-05 | 6.7E-05 | 2.0 | 1.3 | 1.3 | 0.4 | 0.5 | 0.8 |
| Igf1 | Insulin-like growth factor 1 | 9.7E-01 | 7.8E-08 | 0.8 | 1.0 | 1.3 | 1.7 | 2.3 | 2.3 |
| Mef2c | myocyte enhancer factor 2C | 5.1E-05 | 6.3E-02 | 1.5 | 1.4 | 1.4 | 0.5 | 0.8 | 1.1 |
| Mybph | myosin binding protein H | 5.4E-06 | 1.7E-02 | 0.3 | 0.4 | 1.0 | 0.6 | 1.5 | 5.2 |
| Myh1 | myosin, heavy polypeptide 1 | 2.1E-01 | 4.2E-01 | 1.0 | 1.0 | 0.9 | 0.9 | 0.9 | 1.1 |
| Myh2 | myosin, heavy polypeptide 2 | 2.4E-02 | 1.2E-02 | 1.0 | 0.9 | 1.0 | 0.7 | 0.8 | 1.0 |
| Myh3 | myosin, heavy polypeptide 3 | 3.3E-07 | 4.2E-01 | 0.5 | 0.3 | 0.5 | 0.9 | 1.2 | 1.3 |
| Myh4 | myosin, heavy polypeptide 4 | 1.9E-01 | 2.6E-02 | 1.0 | 1.0 | 1.0 | 0.7 | 0.8 | 0.9 |
| Myh7 | myosin, heavy polypeptide 7 | 2.1E-03 | 1.1E-02 | 1.1 | 0.8 | 0.6 | 0.2 | 0.6 | 0.9 |
| Myl2 | myosin, light polypeptide 2, | 9.9E-12 | 4.0E-10 | 0.8 | 0.5 | 0.6 | 0.1 | 0.2 | 0.4 |
| Myl3 | myosin, light polypeptide 3 | 7.8E-06 | 1.3E-09 | 1.0 | 0.6 | 0.7 | 0.3 | 0.2 | 0.4 |
| Myog | myogenin | 4.7E-01 | 4.0E-11 | 0.9 | 1.0 | 1.4 | 3.6 | 1.7 | 1.8 |
| Myom2 | myomesin 2 | 3.1E-03 | 5.6E-05 | 1.2 | 1.0 | 1.0 | 0.6 | 0.7 | 1.1 |
| Tnnc1 | troponin C, cardiac/slow skeletal | 3.4E-03 | 2.3E-02 | 1.1 | 0.7 | 0.7 | 0.5 | 0.6 | 0.7 |
| Tnnc2 | troponin C2, fast | 2.3E-01 | 3.2E-01 | 0.9 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Tnni1 | troponin I, skeletal, slow 1 | 1.3E-08 | 3.8E-01 | 0.8 | 0.5 | 0.5 | 0.6 | 0.8 | 1.0 |
| Tnni2 | troponin I, skeletal, fast 2 | 3.6E-02 | 4.6E-05 | 1.1 | 0.9 | 0.6 | 0.5 | 0.6 | 0.4 |
| Tnnt1 | troponin T1, skeletal, slow | 1.4E-03 | 9.7E-01 | 1.1 | 0.7 | 0.6 | 0.6 | 1.1 | 1.6 |
| Tnnt3 | troponin T3, skeletal, fast | 3.1E-01 | 3.1E-01 | 1.1 | 1.1 | 0.9 | 1.0 | 1.0 | 0.9 |
| Tpm1 | tropomyosin 1, alpha | 1.6E-02 | 2.1E-06 | 0.7 | 0.9 | 1.1 | 1.4 | 1.5 | 1.7 |
| Tpm2 | tropomyosin 2, beta | 1.6E-08 | 1.5E-12 | 1.0 | 0.8 | 0.8 | 0.4 | 0.4 | 0.8 |
| Tpm3 | tropomyosin 3, gamma | 5.7E-01 | 2.8E-07 | 0.7 | 1.1 | 1.2 | 2.5 | 1.6 | 1.6 |
| Tpm4 | tropomyosin 4 | 3.5E-05 | 2.5E-09 | 0.5 | 0.8 | 1.2 | 2.8 | 2.3 | 1.9 |
| Lysosomal Function | |||||||||
| Apg4d | APG4 (ATG4) autophagy-related homolog D | 8.6E-10 | 9.5E-08 | 0.7 | 0.8 | 0.7 | 0.6 | 0.7 | 0.7 |
| Ctsc | cathepsin C | 2.5E-02 | 1.2E-14 | 1.0 | 1.1 | 1.5 | 4.2 | 2.0 | 1.4 |
| Lamp2 | lysosomal membrane glycoprotein 2 | 3.8E-02 | 5.8E-10 | 1.2 | 1.1 | 1.0 | 2.3 | 2.4 | 2.3 |
| Lip1 | lysosomal acid lipase 1 | 5.4E-01 | 1.7E-13 | 0.9 | 1.0 | 1.3 | 3.6 | 2.2 | 1.9 |
| Naglu | alpha-N-acetylglucosaminidase | 3.6E-06 | 1.2E-12 | 1.5 | 1.1 | 1.1 | 1.9 | 1.7 | 1.8 |
| Npc2 | Niemann Pick type C2 | 3.7E-02 | 4.9E-14 | 1.0 | 1.0 | 1.2 | 2.9 | 1.9 | 1.6 |
| Ctsb | cathepsin B | 7.1E-01 | 8.8E-16 | 0.9 | 1.0 | 1.1 | 3.3 | 1.7 | 1.4 |
| Ctsc | cathepsin C | 2.5E-02 | 1.2E-14 | 1.0 | 1.1 | 1.5 | 4.2 | 2.0 | 1.4 |
| Ctse | cathepsin E | 9.9E-01 | 1.7E-03 | 0.9 | 1.0 | 1.2 | 0.6 | 0.9 | 0.5 |
| Ctsh | cathepsin H | 7.2E-01 | 7.2E-14 | 0.7 | 1.0 | 1.4 | 6.6 | 3.0 | 2.2 |
| Ctsk | cathepsin K | 1.2E-04 | 1.9E-14 | 1.6 | 1.1 | 1.5 | 2.7 | 8.3 | 8.4 |
| Ctss | cathepsin S | 7.5E-03 | 1.0E-16 | 0.8 | 1.4 | 1.9 | 15.8 | 4.3 | 2.6 |
| Ctsz | cathepsin Z | 4.1E-01 | 3.8E-12 | 0.9 | 1.0 | 1.2 | 3.0 | 2.0 | 1.5 |
| Gla | galactosidase, alpha | 4.5E-01 | 1.2E-02 | 1.0 | 1.0 | 1.2 | 3.4 | 1.2 | 1.1 |
| Glb1 | galactosidase, beta 1 | 8.4E-03 | 3.1E-07 | 0.8 | 0.9 | 0.8 | 2.9 | 1.7 | 1.8 |
| Gusb | glucuronidase, beta | 7.6E-02 | 4.4E-12 | 0.7 | 0.9 | 1.1 | 3.7 | 1.6 | 1.4 |
| Hexa | hexosaminidase A | 8.1E-03 | 6.5E-15 | 0.8 | 1.0 | 1.0 | 2.5 | 1.8 | 1.5 |
| Hexb | hexosaminidase B | 4.4E-01 | 4.9E-12 | 1.1 | 1.1 | 1.0 | 7.0 | 2.9 | 2.5 |
| Lip1 | lysosomal acid lipase 1 | 5.4E-01 | 1.7E-13 | 0.9 | 1.0 | 1.3 | 3.6 | 2.2 | 1.9 |
| Man1a | mannosidase 1, alpha | 4.2E-01 | 4.0E-09 | 0.9 | 0.9 | 1.3 | 2.3 | 2.1 | 1.8 |
| Psap | prosaposin | 3.6E-01 | 1.0E-07 | 1.0 | 1.0 | 1.0 | 1.6 | 1.1 | 1.0 |
| Proteasome Function | |||||||||
| Psmc1 | protease 26S subunit, ATPase 1 | 1.7E-14 | 4.2E-01 | 1.6 | 1.3 | 1.1 | 1.1 | 1.0 | 1.0 |
| Psmc4 | proteasome 26S subunit, ATPase, 4 | 4.8E-09 | 4.7E-01 | 1.6 | 1.2 | 1.0 | 1.2 | 0.9 | 1.0 |
| Psmd2 | proteasome 26S subunit, non-ATPase, 2 | 2.5E-13 | 2.2E-02 | 1.3 | 1.6 | 1.1 | 1.3 | 1.0 | 1.0 |
| Ubc | ubiquitin C | 2.0E-06 | 5.9E-04 | 2.7 | 1.3 | 1.0 | 0.7 | 0.7 | 0.7 |
| Fbxo32 | F-box only protein 32 | 6.38E-09 | 0.0819765 | 2.7 | 1.9 | 1.3 | 1.5 | 1.3 | 0.8 |
| Trim63 | tripartite motif-containing 63 | 1.08E-05 | 0.1525747 | 1.9 | 1.1 | 1.0 | 1.6 | 1.0 | 0.9 |