Table SI. List of differentially expressed proteins selected from previous proteomic studies for Kyoto Encyclopedia for Genes and Genomes pathway analysis.
A, LF (decreased expression)
Gene GeneID Species
Thrombospondin-4 450,172 Chimpanzee Nascent polypeptide-associated complex subunit α-2 454,797 Chimpanzee Microfibril-associated glycoprotein 4 744,007/454,500 Chimpanzee α-2 type I collagen 105,370,705 Human Asporin 54,829 Human Acetyl-CoA acetyltransferase 38/39 Human Mimecan 4,969 Human Fibulin-5 453,112 Chimpanzee α-1 type I collagen 107,984,355 Human Serum albumin 213 Human
B, LF (increased expression)
Gene GeneID Species
Actin, aortic smooth muscle 59 Human α-1-antichymotrypsin 453,133 Chimpanzee Angiopoietin-related protein 1 74,0954 Chimpanzee Apolipoprotein A-I 335 Human Apolipoprotein B-100 338 Human Apolipoprotein C-III 345 Human ATP-binding cassette sub-family D member 3 100,172,102 Sumatran orangutan Carbonic anhydrase 1 759 Human Cartilage intermediate layer protein 1 8,483 Human Cathelicidin 820 Human Chondroadherin 1,101 Human Type VIII collagen 105,378,949 Human Type VI collagen 1,291 Human Complement C3 718 Human Dihydropyrimidinase 1,807 Human Fibrinogen 2,243/2,244/2,266 Human G protein-activated inward rectifier potassium channel 4 469,548/451,660 Chimpanzee Hemoglobin 3,048/3,039/3,049/3,047/3,044/3,042/ Human 3,046/3,050/3,040/3,045/3,043 Immunoglobulin Not applicable Human Inter-α-trypsin inhibitor 3,697/3,698/3,699/3,700 Human Lamin-A/C 100,757,316 Chinese hamster Lipopolysaccharide-binding protein 3,929 Human Aggrecan core protein 453,629 Chimpanzee α-1-antitrypsin 5,265 Human Annexin A1 301 Human Apolipoprotein A-IV 337 Human Apolipoprotein C-I 341 Human Apolipoprotein E 348 Human Bullous pemphigoid antigen 1 8,354,651 Schistosoma mansoni Carboxypeptidase B2 1,361 Human Cartilage oligomeric matrix protein 1,311 Human Cathepsin G 1,511 Human Clusterin 1,191 Human Type XV collagen 1,306 Human Complement C1q subcomponent subunit B 713 Human Complement C4-A 462,577 Chimpanzee Ferritin 2,495/2,512 Human Table SI. Continued.
Gene GeneID Species
Fibronectin 2,335 Human Glia-derived nexin 5,270 Human Hyaluronan and proteoglycan link protein 1 1,404 Human Insulin-like growth factor-binding protein 3,486/3,483 Human Lactadherin 4,240 Human Latent-transforming growth factor 459,143 Chimpanzee Lysozyme 4,069 Human
C, AF soluble (decreased expression)
Gene GeneID Species
Collagen Type I Alpha 1 Chain 1,277 Human Collagen Type II Alpha 1 Chain 1,280 Human Collagen Type VI Alpha 3 Chain 1,293 Human Biglycan 633 Human Lysozyme 4,069 Human Collagen Type I Alpha 2 Chain 1,278 Human Collagen Type VI Alpha 2 Chain 1,292 Human Collagen Type XI Alpha 2 Chain 1,302 Human Angiogenin 283 Human
D, AF soluble (increased expression)
Gene GeneID Species
Lumican 4,060 Human Thrombospondin 1 7,057 Human Superoxide Dismutase 3 6,649 Human Fibronectin 2,335 Human Clusterin 1,191 Human Milk Fat Globule-EGF Factor 8 Protein 4,240 Human
E, AF insoluble (decreased expression)
Gene GeneID Species
Collagen Type II Alpha 1 Chain 1,280 Human Collagen Type XI Alpha 2 Chain 1,302 Human Collagen Type XI Alpha 1 Chain 1,301 Human
F, AF insoluble (increased expression)
Gene GeneID Species
Collagen Type III Alpha 1 Chain 1,281 Human Decorin 1,634 Human Fibronectin 2,335 Human Clusterin 1,191 Human Aggrecan 176 Human Proline and Arginine Rich End Leucine Rich Repeat Protein 5,549 Human Cartilage Oligomeric Matrix Protein 1,311 Human
G, NP soluble (decreased expression)
Gene GeneID Species
Collagen Type II Alpha 1 Chain 1,280 Human Hyaluronan And Proteoglycan Link Protein 1 1,404 Human Table SI. Continued.
Gene GeneID Species
Lysozyme 4,069 Human Serpin Family A Member 1 5,265 Human Chondroadherin 1,101 Human Angigenin 283 Human Fibroblast Growth Factor Binding Protein 2 83,888 Human Synaptotagmin Like 1 84,958 Human
H, NP soluble (increased expression)
Gene GeneID Species
Biglycan 633 Human Lumican 4,060 Human Proline and Arginine Rich End Leucine Rich Repeat Protein 5,549 Human Cartilage Oligomeric Matrix Protein 1,311 Human Proteoglycan 4 10,216 Human Clusterin 1,191 Human Serpin Family E Member 2 5,270 Human Decorin 1,634 Human Osteoglycin 4,969 Human Fibronectin 2,335 Human ABI Family Member 3 Binding Protein 25,890 Human Phospholipase A2 Group IIA 5,320 Human Superoxide Dismutase 3 6,649 Human
I, NP insoluble (decreased expression)
Gene GeneID Species
Collagen Type I Alpha 1 Chain 1,277 Human Collagen Type I Alpha 2 Chain 1,278 Human
J, NP insoluble (increased expression)
Gene GeneID Species
Lumican 4,060 Human Fibronectin 2,335 Human Clusterin 1,191 Human Proline and Arginine Rich End Leucine Rich Repeat Protein 5,549 Human Cartilage Oligomeric Matrix Protein 1,311 Human
Gene IDs from Kyoto Encyclopedia of Genes and Genomes Database. AF, annulus fibrosus; LF, ligamentum flavum; NP, nucleus pulposus. Table SII. Patient information for the KEGG pathway analysis of differentially expressed proteins based on previous proteomic studies.
Patients information of proteomic analysis about LF.
A, Lumbar spinal stenosis
Sex Number Age
Male 28 71±14 Female 26 70±20
B, Lumbar herniation (control)
Sex Number Age
Male 11 46±31 Female 8 55±20
Patients information of proteomic analysis about AF (Soluble and Insoluble) and NP (Soluble and Insoluble)
Disorder Age Sex IVD level
Scoliosis (control) 11 Female L3-L4 Scoliosis (control) 16 Female L2-L3 Scoliosis (control) 21 Female L2-L3 Scoliosis (control) 25 Female L1-L2 Scoliosis (control) 29 Male L2-L3 Trauma (control) 35 Male L1-L2 Scoliosis (control) 46 Female T12-L1 Disc degeneration 16 Male L4-L5 Disc degeneration 20 Male L4-L5 Disc degeneration 32 Female L4-L5 Disc degeneration 37 Female L4-L5 Disc degeneration 43 Female L4-L5 Disc degeneration 43 Female L4-L5 Disc degeneration 47 Male L4-L5 Disc degeneration 53 Female L4-L5 Table SIII. KEGG pathway enrichment analysis of differentially expressed pathways in LFH and in AF and NP degeneration.
Input Background Term ID number number P-value Input Gene ID
Complement and coagulation cascades hsa04610 8 79 5.66x10-13 5,265|718|1,191|713|1,361| 2,244|2,266|2,243 African trypanosomiasis hsa05143 4 35 2.99x10-7 335|3,040|3,043|3,039 Fat digestion and absorption hsa04975 4 41 5.38x10-7 335|39|337|338 Malaria hsa05144 4 49 1.05x10-6 3,040|3,043|3,039|1,311 ECM-receptor interaction hsa04512 4 82 7.34x10-6 1,291|2,335|1,311|1,101 Vitamin digestion and absorption hsa04977 3 24 7.94x10-6 335|337|338 Staphylococcus aureus infection hsa05150 3 57 8.98x10-5 713|2,266|718 Synthesis and degradation of ketone bodies hsa00072 2 10 1.3x10-4 39|38 Focal adhesion hsa04510 4 203 2.3x10-4 1,291|2,335|1,311|1,101 Protein digestion and absorption hsa04974 3 90 3.3x10-4 1,306|1,291|1,361 Terpenoid backbone biosynthesis hsa00900 2 22 5.5x10-4 39|38 Platelet activation hsa04611 3 122 7.8x10-4 2,244|2,266|2,243 Glyoxylate and dicarboxylate metabolism hsa00630 2 28 8.5x10-4 39|38 Butanoate metabolism hsa00650 2 28 8.5x10-4 39|38 Systemic lupus erythematosus hsa05322 3 136 1.06x10-3 713|1,511|718 Propanoate metabolism hsa00640 2 32 1.1x10-3 39|38 PI3K-Akt signaling pathway hsa04151 4 342 1.54x10-3 1,291|2,335|1,311|1,101 Tryptophan metabolism hsa00380 2 40 1.67x10-3 39|38 Pyruvate metabolism hsa00620 2 40 1.67x10-3 39|38 Fatty acid degradation hsa00071 2 44 2x10-3 39|38 Tuberculosis hsa05152 3 179 2.29x10-3 3,929|820|718 Valine, leucine and isoleucine degradation hsa00280 2 48 2.36x10-3 39|38 Fatty acid metabolism hsa01212 2 48 2.36x10-3 39|38 Mineral absorption hsa04978 2 52 2.75x10-3 2,495|2,512 Lysine degradation hsa00310 2 52 2.75x10-3 39|38 PPAR signaling pathway hsa03320 2 72 5.09x10-3 335|345 Pertussis hsa05133 2 75 5.5x10-3 713|718 Salivary secretion hsa04970 2 89 7.6x10-3 4,069|820 Amoebiasis hsa05146 2 100 9.46x10-3 1,511|2,335 Chagas disease (American trypanosomiasis) hsa05142 2 104 1.019x10-2 713|718 Carbon metabolism hsa01200 2 113 1.19x10-2 39|38 Phagosome hsa04145 2 155 2.14x10-2 1,311|718 Nitrogen metabolism hsa00910 1 17 2.546x10-2 759 Pantothenate and CoA biosynthesis hsa00770 1 18 2.686x10-2 1,807 Renin-angiotensin system hsa04614 1 23 3.381x10-2 1,511 beta-Alanine metabolism hsa00410 1 31 4.483x10-2 1,807 Prion diseases hsa05020 1 35 5.029x10-2 713 Drug metabolism-other enzymes hsa00983 1 46 6.515x10-2 1,807 Legionellosis hsa05134 1 55 7.714x10-2 718 p53 signaling pathway hsa04115 1 69 9.55 x10-2 3,486 Leishmaniasis hsa05140 1 74 1.0196x10-1 718 Bacterial invasion of epithelial cells hsa05100 1 78 1.071x10-1 2,335 Small cell lung cancer hsa05222 1 86 1.173x10-1 2,335 Salmonella infection hsa05132 1 86 1.173x10-1 3,929 NF-kappa B signaling pathway hsa04064 1 93 1.2613x10-1 3,929 Pancreatic secretion hsa04972 1 96 1.2988x10-1 1,361 AGE-RAGE signaling pathway in diabetic hsa04933 1 101 1.3611x10-1 2,335 complications Pyrimidine metabolism hsa00240 1 105 1.4106x10-1 1,807 Toll-like receptor signaling pathway hsa04620 1 106 1.4229x10-1 3,929 Vascular smooth muscle contraction hsa04270 1 120 1.5937x10-1 59 Lysosome hsa04142 1 123 1.6299x10-1 1,511 Alzheimer's disease hsa05010 1 168 2.1543x10-1 348 Transcriptional misregulation in cancer hsa05202 1 180 2.2886x10-1 3,486 Herpes simplex infection hsa05168 1 186 2.3549x10-1 718 Proteoglycans in cancer hsa05205 1 205 2.5612x10-1 2,335 Viral carcinogenesis hsa05203 1 205 2.5612x10-1 718 Table SIII. Continued.
Input Background Term ID number number P-value Input Gene ID
Metabolic pathways hsa01100 3 1,243 2.6402x10-1 1,807|39|38 Regulation of actin cytoskeleton hsa04810 1 215 2.6676x10-1 2,335 Neuroactive ligand-receptor interaction hsa04080 1 278 3.3041x10-1 1,511 Pathways in cancer hsa05200 1 397 4.3619x10-1 2,335
Input Background Term ID number number P-value Input
ECM-receptor interaction hsa04512 4 82 1.18x10-7 1,101|1,280|1,311|2,335 Focal adhesion hsa04510 4 203 3.98x10-6 1,101|1,280|1,311|2,335 PI3K-Akt signaling pathway hsa04151 4 342 2.99x10-5 1,101|1,280|1,311|2,335 Proteoglycans in cancer hsa05205 3 205 1.8x10-4 4,060|1,634|2,335 Complement and coagulation cascades hsa04610 2 79 8.4x10-4 1,191|5,265 alpha-Linolenic acid metabolism hsa00592 1 25 1.364x10-2 5,320 Linoleic acid metabolism hsa00591 1 29 1.572x10-2 5,320 Fat digestion and absorption hsa04975 1 41 2.194x10-2 5,320 Ether lipid metabolism hsa00565 1 45 2.401x10-2 5,320 Malaria hsa05144 1 49 2.607x10-2 1,311 Arachidonic acid metabolism hsa00590 1 62 3.274x10-2 5,320 Bacterial invasion of epithelial cells hsa05100 1 78 4.09x10-2 2,335 TGF-beta signaling pathway hsa04350 1 84 4.394x10-4 1,634 Small cell lung cancer hsa05222 1 86 4.495x10-2 2,335 Salivary secretion hsa04970 1 89 4.646x10-2 4,069 Protein digestion and absorption hsa04974 1 90 4.697x10-2 1,280 Glycerophospholipid metabolism hsa00564 1 95 4.949x10-2 5,320 Pancreatic secretion hsa04972 1 96 4.999x10-2 5,320 Amoebiasis hsa05146 1 100 5.2x10-2 2,335 AGE-RAGE signaling pathway in diabetic hsa04933 1 101 5.25x10-2 2,335 complications Vascular smooth muscle contraction hsa04270 1 120 6.198x10-2 5,320 Phagosome hsa04145 1 155 7.922x10-2 1,311 Regulation of actin cytoskeleton hsa04810 1 215 1.080x10-1 2,335 Ras signaling pathway hsa04014 1 228 1.142x10-1 5,320 Pathways in cancer hsa05200 1 397 1.904x10-1 2,335 Metabolic pathways hsa01100 1 1,243 4.869x10-14 5,320
C, NP insoluble
Input Background Term ID number number P-value Input
Protein digestion and absorption hsa04974 6 90 7.72x10-14 1,278|1,281|1,280|1,289| 1,277|1,301 ECM-receptor interaction hsa04512 5 82 2.04 x10-11 1,278|2,335|1,280|1,311|1,277 Focal adhesion hsa04510 5 203 1.68x10-9 1,278|2,335|1,280|1,311|1,277 Amoebiasis hsa05146 4 100 1.44 x10-8 1,278|1,281|2,335|1,277 AGE-RAGE signaling pathway in hsa04933 4 101 1.49 x10-8 1,278|1,281|2,335|1,277 diabetic complications PI3K-Akt signaling pathway hsa04151 5 342 2.17x10-8 1,278|2,335|1,280|1,311|1,277 Platelet activation hsa04611 3 122 4.91x10-6 1,278|1,281|1,277 Proteoglycans in cancer hsa05205 2 205 1.44x10-3 4,060|2,335 Malaria hsa05144 1 49 1.374x10-2 1,311 Bacterial invasion of epithelial cells hsa05100 1 78 2.164x10-2 2,335 Complement and coagulation cascades hsa04610 1 79 2.191x10-2 1,191 Small cell lung cancer hsa05222 1 86 2.38x10-2 2,335 Phagosome hsa04145 1 155 4.232x10-2 1,311 Regulation of actin cytoskeleton hsa04810 1 215 5.815x10-2 2,335 Pathways in cancer hsa05200 1 397 1.0475x10-1 2,335 Table SIII. Continued.
Input Background Term ID number number P-value Input
ECM-receptor interaction hsa04512 7 82 1.40x10-15 1,278|1,280|7,057|1,277| 1,292|1,293|2,335 Focal adhesion hsa04510 7 203 6.42x10-13 1,278|1,280|7,057|1,277| 1,292|1,293|2,335 Protein digestion and absorption hsa04974 6 90 8.29x10-13 1,278|1,280|1,302|1,277| 1,292|1,293 PI3K-Akt signaling pathway hsa04151 7 342 2.28x10-11 1,278|1,280|7,057|1,277|1,292| 1,293|2,335 Amoebiasis hsa05146 3 100 7.50x10-6 1,278|2,335|1,277 AGE-RAGE signaling pathway in hsa04933 3 101 7.72x10-6 1,278|2,335|1,277 diabetic complications Proteoglycans in cancer hsa05205 3 205 6.12x10-5 4,060|7,057|2,335 Platelet activation hsa04611 2 122 9.9x10-4 1,278|1,277 Bladder cancer hsa05219 1 41 1.573x10-2 7,057 Malaria hsa05144 1 49 1.869x10-2 7,057 p53 signaling pathway hsa04115 1 69 2.608x10-2 7,057 Bacterial invasion of epithelial cells hsa05100 1 78 2.939x10-2 2,335 Complement and coagulation cascades hsa04610 1 79 2.975x10-2 1,191 TGF-beta signaling pathway hsa04350 1 84 3.159x10-2 7,057 Small cell lung cancer hsa05222 1 86 3.232x10-2 2,335 Salivary secretion hsa04970 1 89 3.341x10-2 4,069 Phagosome hsa04145 1 155 5.725x10-2 7,057 Rap1 signaling pathway hsa04015 1 211 7.705x10-2 7,057 Regulation of actin cytoskeleton hsa04810 1 215 7.845x10-2 2,335 MicroRNAs in cancer hsa05206 1 299 1.0737x10-1 7,057 Pathways in cancer hsa05200 1 397 1.4005x10-1 2,335
Input Background Term ID number number P-value Input
Protein digestion and absorption hsa04974 4 90 6.08x10-9 1,281|1,280|1,302|1,301 ECM-receptor interaction hsa04512 3 82 1.12x10-6 1,280|1,311|2,335 Focal adhesion hsa04510 3 203 1.60x10-5 1,280|1,311|2,335 PI3K-Akt signaling pathway hsa04151 3 342 7.42x10-5 1,280|1,311|2,335 Amoebiasis hsa05146 2 100 2.9x10-4 1,281|2,335 AGE-RAGE signaling pathway in hsa04933 2 101 3x10-4 1,281|2,335 diabetic complications Proteoglycans in cancer hsa05205 2 205 1.18x10-3 1,634|2,335 Malaria hsa05144 1 49 1.25x10-2 1,311 Bacterial invasion of epithelial cells hsa05100 1 78 1.969x10-2 2,335 Complement and coagulation cascades hsa04610 1 79 1.994x10-2 1,191 TGF-beta signaling pathway hsa04350 1 84 2.117x10-2 1,634 Small cell lung cancer hsa05222 1 86 2.16x10-2 2,335 Platelet activation hsa04611 1 122 3.05x10-2 1,281 Phagosome hsa04145 1 155 3.855x10-2 1,311 Regulation of actin cytoskeleton hsa04810 1 215 5.301x10-2 2,335 Pathways in cancer hsa05200 1 397 9.57x10-2 2,335
Databases used: KEGG PATHWAY, Gene Ontology Slim, Gene Ontology. Statistical test method: Hypergeometric test/Fisher's exact test. False discovery rate correction method: Benjamini and Hochberg. AF, annulus fibrosus; KEGG, Kyoto Encyclopedia of Genes and Genomes; LF, ligamentum flavum; NP, nucleus pulposus.