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Table 3 Detailed information regarding protein identification and expression pattern in striatum, midbrain and cortex tissues of the PINK1-KO (KO) mice in respect to wildtype control mice (WT):

From: Brain region specific mitophagy capacity could contribute to selective neuronal vulnerability in Parkinson's disease

Striatum:            
NCBI access number Gene symbol Number of isoforms Protein name Expression ratio
(KO vs. wt)
T test (p-value) Mowse score Sequence coverage (%) Number of matched peptides Molecular weight (Da) Theoretical pI Functional annotation (KEGG pathway)
gi|6753428 Ckmt1 1 creatine kinase, mitochondrial 1, ubiquitous 1.37 0.0002 235 12 5 46974 8.39 Metabolic pathways; Arginine and proline metabolism
gi|6755929 Uchl1 7 ubiquitin carboxy-terminal hydrolase L1 1.45 0.0008 67 47 9 24822 5.33 Parkinson's disease
gi|3766201 Sucla2 4 ATP-specific succinyl-CoA synthetase beta subunit 1.42 0.001 299 21 6 46215 5.65 Metabolic pathways; Citrate cycle (TCA cycle); Propanoate metabolism;
gi|6678674 Ldhb 5 lactate dehydrogenase 2, B chain 1.37 0.0012 136 51 2 36549 5.7 Metabolic pathways; Propanoate metabolism; Glycolysis/Gluconeogenesis; Pyruvate metabolism;
gi|31980844 Dhrs1 2 dehydrogenase/reductase (SDR family) member 1 1.54 0.0016 395 21 7 33983 8.66  
gi|10946574 Ckb 5 creatine kinase, brain 1.42 0.0018 465 25 8 42686 5.4 Metabolic pathways; Arginine and proline metabolism
gi|112363107 Nefm 7 Neurofilament triplet M protein 0.43 0.0025 56 12 2 95984 4.76 Amyotrophic lateral sclerosis (ALS)
gi|6680117 Gss 3 glutathione synthetase 1.42 0.0035 436 16 8 52214 5.56 Metabolic pathways; Glutathione metabolism;
gi|15277976 Ndrg2 3 N-myc downstream regulated gene 2 1.4 0.0046 93 6 2 40763 5.23  
gi|809561 Actg1 4 gamma-actin 1.32 0.0048 84 5 2 40992 5.56 Regulation of actin cytoskeleton
gi|387422 Mdh2 8 malate dehydrogenase 1.37 0.0079 222 12 4 35588 8.93 Metabolic pathways; Citrate cycle (TCA cycle); Pyruvate metabolism;
gi|14198249 Aldoc 4 Fructose-bisphosphate aldolase C 1.34 0.0097 144 9 3 39307 6.47 Metabolic pathways; Glycolysis/Gluconeogenesis; Pentose phosphate pathway; Fructose and mannose metabolism
gi|13097102 Ddah2 2 dimethylarginine dimethylaminohydrolase 2 1.32 0.0098 183 18 4 29627 5.66  
gi|33859640 Taldo1 3 transaldolase 1 1.34 0.0109 163 12 4 37363 6.57 Metabolic pathways; Pentose phosphate pathway;
gi|6681195 Dlg4 4 postsynaptic density protein 95 0.64 0.0133 38 4 2 80423 5.56 Huntington's disease
gi|6753476 Cnp 1 cyclic nucleotide phosphodiesterase 1 1.42 0.0142 371 21 8 47094 9.08  
gi|27370516 Idh2 6 isocitrate dehydrogenase 2 (NADP+), mitochondrial 1.37 0.0151 221 10 4 50902 8.88 Metabolic pathways; Citrate cycle (TCA cycle); Glutathione metabolism;
gi|54855 Tpi1 25 triosephosphate isomerase 1.36 0.0214 770 42 12 26679 6.9 Metabolic pathways; Glycolysis/Gluconeogenesis; Fructose and mannose metabolism;
gi|12805413 Echs1 2 Echs1 protein 1.31 0.0245 428 26 8 31237 8.76 Metabolic pathways; Propanoate metabolism;
gi|7305485 Sh3gl1 4 SH3-domain GRB2-like 1 1.28 0.0307 136 7 3 41492 5.53 Endocytosis
Midbrain:            
NCBI access number Gene symbol Number of isoforms Protein name Expression ratio (KO vs. wt) T test (p-value) Mowse score Sequence coverage (%) Number of matched peptides Molecular weight (Da) Theoretical pI Functional annotation (KEGG pathway)
gi|13384652 Mecr 1 trans-2-enoyl-CoA reductase, mitochondrial precursor 0.53 0.001 88 4 2 40316 9.34 Metabolic pathways;
gi|6679937 Gapdh 3 similar to glyceraldehyde-3-phosphate dehydrogenase 0.55 0.002 340 19 5 35787 8.44 Metabolic pathways; Glycolysis/Gluconeogenesis;
gi|12849397 Glod4 1 Glyoxalase domain-containing protein 4 0.69 0.003 545 46 11 33296 5.28  
gi|6753428 Ckmt1 2 creatine kinase, mitochondrial 1, ubiquitous 0.77 0.003 123 14 2 46974 8.39 Metabolic pathways;
gi|18017596 Snx4 1 sorting nexin 4 0.39 0.007 140 6 2 51745 5.58  
gi|27369581 Slc25a12 1 solute carrier family 25 (mitochondrial carrier, Aralar), member 12 0.46 0.007 318 9 5 74523 8.43  
gi|21410877 Rap1gap 1 Rap1gap protein 0.72 0.007 62 9 2 45618 5.47  
gi|387129 Mdh1 3 cytosolic malate dehydrogenase 0.74 0.01 145 11 3 36454 6.16 Metabolic pathways; Citrate cycle (TCA cycle); Pyruvate metabolism;
gi|33440467 Pafah1b2 2 Platelet-activating factor acetylhydrolase, isoform 1b, alpha2 subunit 0.72 0.015 91 8 2 25476 5.57 Metabolic pathways;
gi|21759113 Etfa 2 Electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF) 0.61 0.016 455 29 6 35018 8.42  
gi|1915915 Ulip3 1 Ulip3 protein 0.73 0.016 177 12 3 62142 6.39  
gi|31981086 Efhd2 3 EF hand domain containing 2 0.66 0.018 602 45 9 25084 5.07  
gi|18606238 Gsn 1 gelsolin 0.7 0.018 328 9 5 80712 5.83 Regulation of actin cytoskeleton
gi|6671539 Aldoa 4 aldolase 1, A isoform 0.79 0.019 1158 59 17 39331 8.31 Metabolic pathways; Glycolysis/Gluconeogenesis;
gi|6678483 Uba1 1 ubiquitin-activating enzyme E1, Chr X 0.76 0.021 669 13 10 117734 5.43 Parkinson's disease
gi|18152793 Pdhb 1 pyruvate dehydrogenase (lipoamide) beta 0.78 0.021 497 32 11 38912 6.41 Metabolic pathways; Glycolysis/Gluconeogenesis; Citrate cycle (TCA cycle); Pyruvate metabolism;
gi|6755963 Vdac1 3 voltage-dependent anion channel 1 0.66 0.0217 855 51 10 30737 8.62 Parkinson's disease; Huntington's disease; Calcium signaling pathway
gi|6755967 Vdac3 1 voltage-dependent anion channel 3 0.66 0.025 224 20 4 30733 8.96 Parkinson's disease; Huntington's disease; Calcium signaling pathway
gi|2690302 Got2 2 aspartate aminotransferase precursor 0.77 0.027 533 23 8 47382 9.05 Metabolic pathways; Alanine, aspartate and glutamate metabolism
gi|11141704 Sir2L2 1 sirtuin 2 0.48 0.029 51 4 2 43244 8.22  
gi|22902419 Gpd1l 2 glycerol-3-phosphate dehydrogenase 1-like 0.48 0.029 61 4 2 42517 8.22 Glycerophospholipid metabolism
gi|7106301 Mapre1 1 microtubule-associated protein, RP/EB family, member 1 0.56 0.031 193 18 3 29997 5.12  
gi|8567410 Syn2 1 synapsin II 0.61 0.034 70 3 2 52418 7.62  
gi|6671569 Arbp 2 acidic ribosomal phosphoprotein P0 1.41 0.037 196 19 4 34195 5.91  
gi|9845299 Suclg1 1 succinate-CoA ligase, GDP-forming, alpha subunit 1.21 0.039 88 9 2 34953 9.45 Metabolic pathways; Citrate cycle (TCA cycle); Propanoate metabolism
gi|61098212 Uchl1 1 ubiquitin carboxy-terminal hydrolase L1 0.65 0.04 157 16 3 24822 5.14 Parkinson's disease
gi|6754524 Ldha 6 lactate dehydrogenase 1, A chain 0.61 0.046 151 14 3 36475 7.62 Metabolic pathways; Glycolysis/Gluconeogenesis; Pyruvate metabolism; Propanoate metabolism
gi|29789104 Napb 1 N-ethylmaleimide sensitive fusion protein attachment protein beta 0.76 0.046 708 42 10 33536 6.41  
gi|7305027 Eno2 4 enolase 2, gamma neuronal 0.69 0.047 861 43 13 47267 4.99 Metabolic pathways; Glycolysis/Gluconeogenesis;
gi|55931021 Gdi2 3 Gdi2 protein 1.64 0.049 158 13 3 50506 5.93  
Cortex:            
NCBI access number Gene symbol Number of Isoforms Protein name Expression ratio (KO vs. wt) T test (p-value) Mowse score Sequence coverage (%) Number of matched peptides Molecular weight (Da) Theoretical pI Functional annotation (KEGG pathway)
gi|4760600 Ak3 1 adenylate kinase isozyme 3 0.66 0.0004 124 47 11 24625 8.57  
gi|13385942 Cs 5 citrate synthase 0.74 0.0057 130 28 16 51703 8.72 Metabolic pathways;
gi|37700232 Nme1 4 nucleoside-diphosphate kinase 1 1.22 0.0006 91 48 9 17197 6.84 Metabolic pathways;
gi|19547889 Gss 3 glutathione synthetase 1.24 0.0386 107 26 12 51913 6.52 Metabolic pathways;
gi|42542422 Hspa8 5 Heat shock protein 8 1.24 0.0019 180 35 23 68074 5.32  
gi|123230136 Prdx1 1 peroxiredoxin 1 1.24 0.0228 64 23 5 18915 6.82  
gi|37202121 Abat 3 4-aminobutyrate aminotransferase 1.25 0.0005 227 37 24 56416 8.35 Metabolic pathways; Alanine, aspartate and glutamate metabolism; Propanoate metabolism; Valine, leucine and isoleucine degradation
gi|113680348 Fscn1 2 fascin homolog 1, actin bundling protein 1.26 0.0017 168 42 17 54474 6.44  
gi|34784434 Eno1 4 Eno1 protein 1.26 0.0062 139 43 16 39757 5.86 Metabolic pathways; Glycolysis/Gluconeogenesis;
gi|56789289 Ldhb 4 Ldhb protein 1.27 0.0011 86 42 7 11317 5.73 Metabolic pathways; Glycolysis/Gluconeogenesis; Propanoate metabolism; Cysteine and methionine metabolism
gi|6679439 Ppia 4 peptidylprolyl isomerase A 1.3 0.0006 99 53 12 17960 7.74  
gi|6755040 Pfn1 3 profilin 1 1.31 0.0022 176 73 14 14948 8.46 Regulation of actin cytoskeleton
gi|6678469 Tuba1c 2 tubulin, alpha 1C 1.32 0.0000088 98 35 13 49877 4.96  
gi|809561 3 1 gamma-actin 1.32 0.0028 230 56 24 41724 5.3 Regulation of actin cytoskeleton
gi|6679937 Gapdh 6 glyceraldehyde-3-phosphate dehydrogenase 1.33 0.0005 211 60 23 35787 8.44 Metabolic pathways; Glycolysis/Gluconeogenesis;
gi|49868 Actb 2 beta-actin (aa 27-375) 1.35 0.0019 237 54 27 39161 5.79 Regulation of actin cytoskeleton
gi|148686116 Taldo1 2 transaldolase 1, isoform CRA_e 1.39 0.0008 156 51 18 31514 7.66 Metabolic pathways; Pentose phosphate pathway
gi|6678413 Tpi1 1 triosephosphate isomerase 1 1.39 0.0006 147 42 9 26696 6.9 Metabolic pathways; Glycolysis/Gluconeogenesis; Fructose and mannose metabolism
gi|123210063 --- 1 novel protein 1.44 0.0009 38 20 4 24445 8.76  
gi|6755963 Vdac1 1 voltage-dependent anion channel 1 1.47 0.0019 161 62 15 30737 8.62  
gi|6671539 Aldoa 4 aldolase 1, A isoform 1.52 0.005 179 43 17 39331 8.31 Metabolic pathways; Glycolysis/Gluconeogenesis; Pentose phosphate pathway; Fructose and mannose metabolism
gi|1915915 Dpysl1 2 Ulip3 protein 1.56 0.0058 225 40 24 62142 6.39  
gi|20072952 Auh 2 Auh protein 1.62 0.000068 114 32 13 32621 9.57 Metabolic pathways; Valine, leucine and isoleucine degradation
gi|11066098 Tkt 1 transketolase 1.89 0.0058 65 26 11 60545 6.54 Metabolic pathways; Pentose phosphate pathway;
gi|21311871 Nebl 1 nebulette 2.2 0.0007 74 40 13 31093 8.54  
gi|163838648 Atp5c1 1 ATP synthase, H+ transporting, mitochondrial F1 complex, gamma subunit isoform b 2.2 0.0007 126 42 15 30237 8.86 Metabolic pathways;
gi|202423 Pgk1 2 (with divergent regulation) phosphoglycerate kinase 1.54; 0.77 5.00E-03; 1.22E-02 265 58 28 44522 8.02 Metabolic pathways; Glycolysis/Gluconeogenesis;
gi|160298209 Got1 2 (with divergent regulation) glutamate oxaloacetate transaminase 1, soluble 1.62; 0.78 1.12E-02; 2.60E-03 130 30 12 46219 6.68 Metabolic pathways; Alanine, aspartate and glutamate metabolism