Table 4. Genes with recognized function in muscle atrophy, differentiation, or contraction and significantly regulated in space versus ground groups.
| Gene symbol | Protein | Fold change | P-value |
|---|---|---|---|
|
Contractile fibers
| |||
| Abra a | Actin binding rho-activating protein | 3.14 | 0.0046 |
| Actn2a , b | Actinin alpha 2 | 3.01 | 0.0066 |
| Ankrd23 a | Ankyrin repeat domain 23 | 3.10 | 0.0043 |
| Csrp3 a , b | Cysteine and glycine-rich protein 3 | 2.08 | 0.015 |
| Des a , b | Desmin | 2.06 | 0.0063 |
| Flnb | Filamin, beta | 2.38 | 0.015 |
| Flnc | Filamin c, gamma | 3.12 | 0.035 |
| Ldb3 a , b | Lim domain binding 3 | 2.42 | 0.00081 |
| Lmod2 b | Leiomodin 2 (cardiac) | 3.35 | 0.014 |
| Mybpc1 | Myosin-binding protein C, slow type | 2.23 | 0.0097 |
| Mybpc2a | Myosin-binding protein C, fast type | 2.23 | 0.019 |
| Myh2 a | Myosin, heavy polypeptide 2, skeletal muscle, adult | 2.46 | 0.03 |
| Mylk2 | Myosin, light polypeptide kinase 2, skeletal muscle | 17.51 | 0.00003 |
| Myom1 a | Myomesin 1 | 2.42 | 0.0064 |
| Myom2 a , b | Myomesin 2 | 3.40 | 0.0042 |
| Myom3 | Myomesin, family member 3 | 2.15 | 0.027 |
| Myot a | Myotilin | 2.50 | 0.002 |
| Myoz2 a , b | Myozenin 2 | 2.78 | 0.008 |
| Myoz3 | Myozenin 3 | 2.20 | 0.0076 |
| Neb a | Nebulin | 2.48 | 0.0065 |
| Nexn | Nexilin | 2.65 | 0.0021 |
| Nrap | Nebulin-related anchoring protein | 2.38 | 0.012 |
| Obscn a | Obscurin, cytoskeletal calmodulin, and titin-interacting rhogef | 2.99 | 0.0071 |
| Pdlim3 b | PDZ and LIM domain 3 | 3.71 | 0.00018 |
| Pdlim7 | PDZ and LIM domain 7 | 2.15 | 0.015 |
| Sgcg a | Sarcoglycan, gamma (dystrophin-associated glycoprotein) | 2.00 | 0.011 |
| Smtnl1 | Smoothelin-like 1 (localization?) | 2.26 | 0.027 |
| Smyd1 a , b | SET and MYND domain containing 1 | 2.38 | 0.02 |
| Synm | Synemin, intermediate filament protein | 2.80 | 0.00023 |
| Synpo2 | Synaptopodin 2 | 2.57 | 0.0035 |
| Synpo2l a | Synaptopodin 2 like | 2.56 | 0.0025 |
| Tcap b | Titin-cap | 2.07 | 0.0045 |
| Tmod1 | Tropomodulin 1 | 2.26 | 0.0041 |
| Tmod4 a , b | Tropomodulin 4 | 2.37 | 0.0003 |
| Tnni2 a | Troponin 1, skeletal, fast | 2.14 | 0.012 |
| Tpm2 a | Tropomyosin 2, beta | 2.03 | 0.0026 |
| Trim54 | Tripartite motif-containing 54 | 2.46 | 0.0017 |
| Ttn a , b | Titin | 2.04 | 0.018 |
| Xirp1 a | Xin actin-binding repeat containing 1 | 2.87 | 0.042 |
|
Sarcoleme, neuromuscular junction, and excitation–contraction coupling
| |||
| Ank1 | Ankyrin 1, erythroid | 2.03 | 0.0022 |
| Atp2a1 | Atpase, Ca++ transporting, cardiac muscle, fast twitch 1 | 2.06 | 0.016 |
| Cacna1s | Calcium channel, voltage-dependent, L type, alpha 1S subunit | 2.56 | 0.0019 |
| Camk2d | Calcium/calmodulin-dependent protein kinase II delta | 2.22 | 0.0074 |
| Casq1 a | Calsequestrin 1 | 2.50 | 0.011 |
| Cav3 a , b | Caveolin 3 | 2.26 | 0.0067 |
| Hrc a | histidine-rich calcium binding protein | 2.06 | 0.03 |
| Itgb1bp2 b | Integrin beta 1-binding protein 2 | 2.57 | 0.00067 |
| Jph2 a , b | Junctophilin 2 | 2.30 | 0.03 |
| Jsrp1 | Junctional sarcoplasmic reticulum protein 1 | 2.70 | 0.0019 |
| Pacsin3 a | Protein kinase C and casein kinase substrate in neurons 3 | 2.37 | 0.00002 |
| Ryr1 | Ryanodin receptor 1, skeletal muscle | 2.42 | 0.011 |
| Slc8a3 a | Solute carrier family 8 (sodium/calcium exchanger), member 3 | 2.24 | 0.012 |
| Sypl2 | Synaptophysin-like 2 | 2.01 | 0.0071 |
| Trdn a | Triadin | 2.25 | 0.003 |
|
Oxidative phosphorylation, glycogen breakdown, and glycolysis
| |||
| Agl | Amylo-1,6-glucosidase, 4-alpha-glucanotransferase | 2.11 | 0.0057 |
| Ckmt2 a , b | Creatine kinase, mitochondrial 2 (sarcomeric) | 3.30 | 0.0002 |
| Cox6a2 a , b | Cytochrome c oxidase subunit via polypeptide 2 | 2.13 | 0.0077 |
| Eno3 a | Enolase 3, beta muscle | 2.49 | 0.0014 |
| Mb a | Myoglobin | 3.16 | 0.00016 |
| Pfkm | Phosphofructokinase, muscle | 2.52 | 0.0026 |
| Pgam2 a , b | Phosphoglycerate mutase 2 | 2.94 | 0.0012 |
| Phka1 | Phosphorylase kinase alpha 1 | 2.02 | 0.0038 |
| Phkg1 | Phosphorylase kinase gamma 1 | 2.72 | 0.013 |
| Ppp1r3c | Protein phosphatase 1, regulatory (inhibitor) subunit 3C | 2.34 | 0.009 |
| Pygm | Muscle glycogen phosphorylase | 2.71 | 0.0049 |
| Txnip | Thioredoxin interacting protein | 2.07 | 0.023 |
|
Myogenesis and muscle development, and atrophy
| |||
| Abra a | Actin-binding Rho-activating protein | 3.14 | 0.0091 |
| Alpk3 | Alpha-kinase 3 | 2.2 | 0.0039 |
| Asb2 a | Ankyrin repeat and SOCS box containing 2 | 3.58 | 0.0015 |
| Atf3 a | Activating transcription factor 3 | 2.00 | 0.0063 |
| Capn3 a , b | Calpain 3 | 2.03 | 0.0019 |
| Csrp3 a , b | Cysteine and glycine-rich protein 3 | 2.08 | 0.015 |
| Dmrt2 | Doublesex and MAB3-related transcription factor 2 | −2.49 | 0.0027 |
| Fbxo32 b | F-box protein 32 | 2.13 | 0.046 |
| Hspb7 b | Heat shock 27 kDa protein family, member 7 (cardiovascular) | 3.73 | 0.0052 |
| Kbtbd10 a | Kelch repeat and BTB (POZ) domain containing 10 | 3.39 | 0.00063 |
| Lbx1 | Ladybird homeobox 1 | 2.73 | 0.0005 |
| Mef2c a , b | Myocyte enhancer factor 2C | 2.11 | 0.0015 |
| Murc | Muscle-related coiled-coil protein | 2.29 | 0.034 |
| Myf6 a , b | Myogenic factor 6 | 2.22 | 0.0047 |
| Myog a , b | Myogenin | 2.13 | 0.026 |
| Pdlim3 | PDZ and LIM domain 3 | 3.71 | 0.00018 |
| Pdlim7 | PDZ and LIM domain 7 | 2.15 | 0.015 |
| Rbm24 a | RNA binding motif 24 | 3.05 | 0.0011 |
| Serpine 1 a | Plasminogen activator inhibitor 1, PAI 1 | 3.96 | 0.00989 |
| Smyd1 a , b | SET and MYND domain containing 1 | 2.38 | 0.02 |
| Trim63 a , b | Tripartite motif-containing 63 | 4.98 | 0.016 |
| Vgll2 | Vestigial like 2 (drosophila) | 2.23 | 0.028 |
Genes recognized as transcriptional targets or having a recognized or potential binding site for
a
MEF2 and/or
b
myogenin on their promoter.