Table 6.
Most differentially expressed genes between WT vs. MuRF1 KO mice after DEN
| Category | Fold Difference | Effect of DEN | Gene Symbol | Definition | Gene ID |
|---|---|---|---|---|---|
| A. 3d DEN genes expressed at higher levels in MuRF1 KO mice | |||||
| I | 4.09 | D | COPS8 | COP9 (constitutive photomorphogenic), subunit 8) | 108679 |
| I | 3.30 | D | Gm4980 | predicted gene 4980 | 245190 |
| I | 3.27 | D | DDIT4L | DNA-damage-inducible transcript 4-like | 73284 |
| I | 2.93 | D | NEU2 | neuraminidase 2 | 23956 |
| I | 2.80 | D | LOC667597 | unknown | 667597 |
| I | 2.45 | D | CHAC1 | ChaC, cation transport regulator-like 1 (E. coli) | 69065 |
| I | 2.41 | D | THAP4 | THAP domain containing 4 | 67026 |
| I | 2.39 | D | PHKG1 | phosphorylase kinase gamma 1 | 18682 |
| V | 2.18 | U | TMEM100 | transmembrane protein 100 | 67888 |
| I | 2.11 | D | MYH1 | myosin, heavy polypeptide 1, skeletal muscle, adult | 17879 |
| I | 2.07 | D | GPD1 | glycerol-3-phosphate dehydrogenase 1 (soluble) | 14555 |
| I | 2.05 | D | MYLK2 | myosin, light polypeptide kinase 2, skeletal muscle | 228785 |
| B. 3d DEN Genes expressed at higher levels in WT mice | |||||
| III | 3.25 | U | DUPD1 | Dual-specificity phosphatase and proisomerase domain 1 | 435391 |
| III | 2.52 | U | SNHG6 | small nucleolar RNA host gene (nonprotein coding) 6 | 73824 |
| III | 2.44 | U | A630038E17RIK | unknown | 219065 |
| III | 2.38 | U | ORM1 | orosomucoid 1 | 18405 |
| III | 2.36 | U | EGR1 | early growth response 1 | 13653 |
| III | 2.09 | U | GM6462 | predicted gene 6462 | 638892 |
| III | 2.03 | U | GSTA2 | glutathione S-transferase, alpha 2 (Yc2) | 14858 |
| III | 2.02 | U | SIDT1 | SID1 transmembrane family, member 1 | 320007 |
| III | 2.01 | U | GSTA4 | glutathione S-transferase, alpha 4 | 14860 |
| C. 14d DEN Genes expressed at higher levels in MuRF1 KO mice | |||||
| V | 7.39 | U | 2310015A16RIK | unknown | 69561 |
| V | 4.82 | U | CCDC110 | coiled-coil domain containing 110 | 212392 |
| II | 3.40 | U | MT2 | metallothionein 2 | 17750 |
| II | 3.36 | U | CCL8 | chemokine (C-C motif) ligand 8 | 20307 |
| I | 3.23 | D | 9630033F20RIK | unknown | 319801 |
| V | 3.16 | U | LONRF1 | LON peptidase N-terminal domain and ring finger 1 | 244421 |
| II | 3.16 | U | HP | haptoglobin | 15439 |
| I | 3.14 | D | EG245190 | predicted gene 4980 | 100503386 |
| I | 2.96 | D | GNG2 | guanine nucleotide binding protein (G protein), gamma 2 | 14702 |
| V | 2.83 | U | CSRP1 | cysteine and glycine-rich protein 1 | 13007 |
| II | 2.83 | U | CCL7 | chemokine (C-C motif) ligand 7 | 20306 |
| I | 2.77 | D | FCOR | FOXO corepressor | 100503924 |
| II | 2.72 | U | TSC22D3 | TSC22 domain family, member 3, transcript variant 2 | 14605 |
| II | 2.70 | U | MT1 | metallothionein 1 | 17748 |
| I | 2.69 | D | KLHL38 | kelch-like 38 (Drosophila) | 268807 |
| V | 2.68 | U | SSH2 | slingshot homolog 2 (Drosophila) | 237860 |
| I | 2.67 | D | NOS1 | nitric oxide synthase 1, neuronal | 18125 |
| V | 2.63 | U | CAR1 | carbonic anhydrase 1, transcript variant 1. | 12346 |
| II | 2.56 | U | FCER1G | Fc receptor, IgE, high affinity I, gamma polypeptide | 14127 |
| I | 2.54 | D | ZFP467 | zinc finger protein 467, transcript variant 3 | 68910 |
| II | 2.49 | U | SRFBP1 | serum response factor binding protein 1 | 67222 |
| II | 2.40 | U | PLEKHO2 | pleckstrin homology domain containing, family O2 | 102595 |
| II | 2.40 | U | WISP2 | WNT1 inducible signaling pathway protein 2 | 22403 |
| II | 2.34 | U | A430104N18RIK | unknown | 78591 |
| II | 2.33 | D | ADH1 | alcohol dehydrogenase 1 (class I) | 11522 |
| II | 2.32 | U | FBXO32 | F-box protein 32, (MAFbx, atrogin-1) | 67731 |
| II | 2.29 | U | GLUL | glutamate-ammonia ligase (glutamine synthetase) | 14645 |
| I | 2.26 | D | CLEC3B | C-type lectin domain family 3 | 21922 |
| II | 2.22 | U | TRAM2 | translocating chain-associating membrane protein 2 | 170829 |
| II | 2.22 | U | SERPINA3N | serine (or cysteine) peptidase inhibitor, clade A 3N | 20716 |
| V | 2.21 | U | 2900073C17RIK | unknown | 73020 |
| II | 2.20 | U | GPR146 | G protein-coupled receptor 146, transcript variant 1 | 80290 |
| I | 2.19 | D | TUBA8 | tubulin, alpha 8 | 53857 |
| V | 2.14 | U | H2-DMA | histocompatibility 2, class II, locus DMa | 14998 |
| I | 2.14 | D | SEC61B | Sec61 beta subunit | 66212 |
| II | 2.12 | U | BCL2A1B | B-cell leukemia/lymphoma 2 related protein A1b | 12045 |
| I | 2.12 | D | ZMYND17 | PREDICTED: zinc finger, MYND domain containing 17 | 74843 |
| I | 2.09 | D | LRG1 | leucine-rich alpha-2-glycoprotein 1 | 76905 |
| II | 2.06 | U | CCL9 | chemokine (C-C motif) ligand 9 | 20308 |
| II | 2.06 | U | MGL1 | macrophage galactose N-acetyl-galactosamine lectin 1 | 17312 |
| V | 2.04 | U | OLIG1 | oligodendrocyte transcription factor 1 | 50914 |
| II | 2.03 | U | H2-AA | histocompatibility 2, class II antigen A, alpha | 14960 |
| I | 2.02 | D | CIDEC | cell death-inducing DFFA-like effector c | 14311 |
| D. 14d DEN Genes expressed at higher levels in WT mice | |||||
| III | 5.74 | U | NRCAM | neuron-glia-CAM-related cell adhesion molecule | 319504 |
| III | 4.08 | U | AIF1L | allograft inflammatory factor 1-like | 108897 |
| III | 3.85 | U | GSTA1 | glutathione S transferase A1 | 14857 |
| III | 3.55 | U | FAM83D | family with sequence similarity 83, member D | 71878 |
| III | 3.51 | U | KRT8 | keratin 8 | 16691 |
| III | 3.02 | U | CHRND | cholinergic receptor, nicotinic, delta polypeptide | 11447 |
| III | 2.99 | U | CHRNG | cholinergic receptor, nicotinic, gamma polypeptide | 11449 |
| III | 2.99 | U | HAUS8 | HAUS augmin-like complex, subunit 8 | 76478 |
| III | 2.94 | U | STAC2 | SH3 and cysteine rich domain 2 | 217154 |
| III | 2.75 | U | UCHL1 | ubiquitin carboxy-terminal hydrolase L1 | 22223 |
| III | 2.65 | U | EPHX4 | epoxide hydrolase 4 | 384214 |
| III | 2.58 | U | 1700029J07RIK | unknown | 69479 |
| III | 2.57 | U | ATP13A3 | PREDICTED: ATPase type 13A3, transcript variant 1 | 224088 |
| III | 2.54 | U | PLEKHB2 | pleckstrin homology domain containing B2 | 226971 |
| III | 2.52 | U | ITGA9 | integrin A9 | 104099 |
| III | 2.49 | U | MTAP1B | microtubule-associated protein 1 B | 17755 |
| III | 2.42 | U | DUSP4 | dual specificity phosphatase 4 | 319520 |
| IV | 2.40 | D | DUSP18 | dual specificity phosphatase 18 | 75219 |
| III | 2.37 | U | HIP1R | huntingtin interacting protein 1 related | 29816 |
| III | 2.37 | U | 9330102E08RIK | unknown | 330427 |
| III | 2.34 | U | DUPD1 | dual specificity phosphatase/pro isomerase 1 | 435391 |
| III | 2.31 | U | UGCG | UDP-glucose ceramide glucosyltransferase | 22234 |
| IV | 2.31 | D | 9930105H17RIK | unknown | 100669 |
| IV | 2.27 | D | NAPEPLD | N-acyl phosphatidylethanolamine phospholipase D | 242864 |
| III | 2.27 | U | BC034090 | unknown | 207792 |
| III | 2.26 | U | HHIPL1 | hedgehog interacting protein-like 1 | 214305 |
| III | 2.26 | U | MFHAS1 | malignant fibrous histiocytoma amplified seq 1 | 52065 |
| III | 2.22 | U | MNS1 | meiosis-specific nuclear structural protein 1 | 17427 |
| III | 2.21 | U | LRP11 | low density lipoprotein receptor-related protein 11 | 237253 |
| III | 2.17 | U | C230098O21RIK | unknown | 102153 |
| III | 2.17 | U | BPIFB1 | BPI fold containing family B, member 1 | 228801 |
| III | 2.10 | U | KRT18 | keratin 18 | 16668 |
| III | 2.07 | U | VASP | vasodilator-stimulated phosphoprotein | 22323 |
| III | 2.06 | U | MYH3 | myosin, heavy polypeptide 3, skeletal muscle | 17883 |
| III | 2.05 | U | SH3RF1 | SH3 domain containing ring finger 1 | 59009 |
| III | 2.04 | U | XRRA1 | PREDICTED: X-ray radiation resistance associated 1 | 446101 |
| III | 2.04 | U | MUSK | muscle, skeletal, receptor tyrosine kinase, variant 5 | 18198 |
| III | 2.01 | U | SH3D19 | PREDICTED: SH3 domain protein D19, variant 2 | 27059 |
A: genes whose average signal is significantly higher in MuRF1 KO mice after 3d of DEN. B: genes whose average signal is significantly higher in WT mice after 3d of DEN. C: genes whose average signal is significantly higher in MuRF1 KO mice after 14d of denervation. D: genes whose average signal is significantly higher in WT mice after 14d of DEN. Genes localized near MuRF1 on chromosome 4 are excluded from analysis, and only genes up (U)- or downregulated (D) by DEN are included. Category I genes show delayed repression in MuRF1 KO mice but are equally repressed in both genotypes at 14d; category II genes are upregulated at 3d in both genotypes but remain elevated in MuRF1 KO mice at 14d; category III genes are upregulated to a lesser extent in MuRF1 KO mice than in WT mice; category IV genes are downregulated to a greater extent in MuRF1 KO mice at either 3d or 14d; category V genes are upregulated to a greater extent in MuRF1 KO mice at 3d or both 3d and 14d.