Identification of genes associated with osteoarthritis by microarray analysis

Molecular Medicine Reports

Volumn 12, Issue 4, 2015, Pages 5211-5216

  Sun, Jianwei ^a   Yan, Bingshan ^a   Yin, Wangping ^a   Zhang, Xinchao ^a  

^a JINSHAN HOSPITAL OF FUDAN UNIVERSITY   (China)

Author keywords

Enrichment analysis; Module analysis; Osteoarthritis; Protein domain enrichment analysis

Indexed keywords

ADAMTS1 PROTEIN; BUB1 RELATED PROTEIN; BUB1B PROTEIN; CCNB1 PROTEIN; CD36 ANTIGEN; COL11A2 PROTEIN; COL1A1 PROTEIN; COL2A1 PROTEIN; COL3A1 PROTEIN; CYCLIN A2; FIBROBLAST GROWTH FACTOR 19; KIF11 PROTEIN; KIF2C PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CELL CYCLE; CELLULAR STRESS RESPONSE; DOWN REGULATION; EXTRACELLULAR MATRIX; GENE EXPRESSION; GENE IDENTIFICATION; HUMAN; MICROARRAY ANALYSIS; MITOSIS; NITROGEN METABOLISM; NUCLEOTIDE SEQUENCE; OSTEOARTHRITIS; PATHOGENESIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; UPREGULATION; BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC ASSOCIATION STUDY; GENETICS; METABOLISM; NUCLEIC ACID DATABASE; PROTEIN ANALYSIS;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC ASSOCIATION STUDIES; HUMANS; OSTEOARTHRITIS; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS;

EID: 84940500853     PISSN: 17912997     EISSN: 17913004     Source Type: Journal    
DOI: 10.3892/mmr.2015.4048     Document Type: Article

References (40)

1. Fransen M, Bridgett L, March L, Hoy D, Penserga E and Brooks P: The epidemiology of osteoarthritis in Asia. Int J Rheum Dis 14: 113-121, 2011.
2. Mahjoub M, Berenbaum F and Houard X: Why subchondral bone in osteoarthritis? The importance of the cartilage bone interface in osteoarthritis. Osteoporos Int 23 (Suppl 8): S841-S846, 2012.
3. Henrotin Y, Pesesse L and Sanchez C: Subchondral bone and osteoarthritis: Biological and cellular aspects. Osteoporos Int 23: S847-S851, 2012.
4. Chou CH, Wu CC, Song IW, Chuang H P, Lu LS, Chang JH, Kuo SY, Lee CH, Wu JY, Chen YT, et al: Genome-wide expression profiles of subchondral bone in osteoarthritis. Arthritis Res Ther 15: R190, 2013.
5. Chou CH, Wu CC, Song IW, Chuang H P, Lu LS, Chang JH, Kuo SY, Lee CH, Wu JY and Chen YT: Genome-wide expression profiles of subchondral bone in osteoarthritis. Arthritis Res Ther 15: R190, 2013.
6. Zhen G, Wen C, Jia X, Li Y, Crane JL, Mears SC, Askin FB, Frassica FJ, Chang W, Yao J, et al: Inhibition of TGF-β signaling in mesenchymal stem cells of subchondral bone attenuates osteo-arthritis. Nat Med 19: 704-712, 2013.
7. Valverde-Franco G, Pelletier J P, Fahmi H, Hum D, Matsuo K, Lussier B, Kapoor M and Martel-Pelletier J: In vivo bone-specifc EphB4 overexpression in mice protects both subchondral bone and cartilage during osteoarthritis. Arthritis Rheum 64: 3614-3625, 2012.
8. Karlsson C, Dehne T, Lindahl A, Brittberg M, Pruss A, Sittinger M and Ringe J: Genome-wide expression profiling reveals new candidate genes associated with osteoarthritis. Osteoarthritis Cartilage 18: 581-592, 2010.
9. Gautier L, Cope L, Bolstad BM and Irizarry RA: Affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20: 307-315, 2004.
10. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U and Speed TP: Exploration, normalization and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264, 2003.
11. Smyth G and Limma: Linear models for microarray data Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005. Springer, New York, pp 397-420, 2005.
12. Benjamini Y and Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc 57: 289-300, 1995.
13. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis A P, Dolinski K, Dwight SS, Eppig JT, et al: Gene Ontology: Tool for the unifcation of biology. The gene ontology consortium. Nat Genet 25: 25-29, 2000.
14. Kanehisa M and Goto S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30, 2000.
15. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C and Jensen LJ: STRING v9. 1: Protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41 (Detabase Issue): D808-D815, 2013.
16. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD and Ideker T: A travel guide to Cytoscape plugins. Nat Methods 9: 1069-1076, 2012.
17. Adamcsek B, Palla G, Farkas IJ, Derényi I and Vicsek T: CFinder: Locating cliques and overlapping modules in biological networks. Bioinformatics 22: 1021-1023, 2006.
18. Derényi I, Palla G, and Vicsek T: Clique percolation in random networks. Phys Rev Lett 94: 160202, 2005.
19. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, et al: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 29: 37-40, 2001.
20. Tew SR, Kwan AP, Hann A, Thomson BM and Archer CW: The reactions of articular cartilage to experimental wounding: Role of apoptosis. Arthritis Rheum 43: 215-225, 2000.
21. Costouros JG and Kim HT: Preventing chondrocyte programmed cell death caused by iatrogenic injury. Knee 14: 107-111, 2007.
22. Khan IM, Palmer EA and Archer CW: Fibroblast growth factor-2 induced chondrocyte cluster formation in experimentally wounded articular cartilage is blocked by soluble Jagged-1. Osteoarthritis Cartilage 18: 208-219, 2010.
23. Moore EE, Bendele AM, Thompson DL, Littau A, Waggie KS, Reardon B and Ellsworth JL: Fibroblast growth factor-18 stimulates chondrogenesis and cartilage repair in a rat model of injury-induced osteoarthritis. Osteoarthritis Cartilage 13: 623-631, 2005.
24. Zhu C, Zhao J, Bibikova M, Leverson JD, Bossy-Wetzel E, Fan JB, Abraham RT and Jiang W: Functional analysis of human microtubule-based motor proteins, the kinesins and dyneins, in mitosis/cytokinesis using RNA interference. Mol Biol Cell 16: 3187-3199, 2005.
25. Min BJ, Kim N, Chung T, Kim OH, Nishimura G, Chung CY, Song HR, Kim HW, Lee HR, Kim J, et al: Whole-exome sequencing identifes mutations of KIF22 in spondyloepime-taphyseal dysplasia with joint laxity, leptodactylic type. Am J Hum Genet 89: 760-766, 2011.
26. Boyden ED, Campos-Xavier AB, Kalamajski S, Cameron TL, Suarez P, Tanackovic G, Andria G, Ballhausen D, Briggs MD, Hartley C, et al: Recurrent dominant mutations affecting two adjacent residues in the motor domain of the monomeric kinesin KIF22 result in skeletal dysplasia and joint laxity. Am J Hum Genet 89: 767-772, 2011.
27. Sun Y, Mauerhan DR, Franklin AM, Norton J, Hanley EN Jr and Gruber HE: Phosphocitrate is potentially a disease-modifying drug for noncrystal-associated osteoarthritis. Biomed Res Int 2013: 326267, 2013.
28. Sun Y, Roberts A, Mauerhan DR, Sun AR, Norton HJ and Hanley EN Jr: Biological activities of phosphocitrate: A potential meniscal protective agent. Biomed Res Int 2013: 726581, 2013.
29. Taylor SS and Mckeon F: Kinetochore localization of murine Bub1 is required for normal mitotic timing and checkpoint response to spindle damage. Cell 89: 727-735, 1997.
30. Davenport JW, Fernandes ER, Harris LD, Neale GA and Goorha R: The mouse mitotic checkpoint gene bub1b, a novel bub1 family member, is expressed in a cell cycle-dependent manner. Genomics 55: 113-117, 1999.
31. Sartor H, Ehlert F, Grzeschik KH, Müller R and Adolph S: Assignment of two human cell cycle genes, CDC25C and CCNB1, to 5q31 and 5q12, respectively. Genomics 13: 911-912, 1992.
32. Zhang C, Wang L, Wu D, Chen H, Chen Z, Thomas-Ahner JM, Zynger DL, Eeckhoute J, Yu J, Luo J, et al: Definition of a FoxA1 Cistrome that is crucial for G1 to S-phase cell-cycle transit in castration-resistant prostate cancer. Cancer Res 71: 6738-6748, 2011.
33. Van Der Kraan PM, Buma P, Van Kuppevelt T and Van Den Berg WB: Interaction of chondrocytes, extracellular matrix and growth factors: Relevance for articular cartilage tissue engineering. Osteoarthritis Cartilage 10: 631-637, 2002.
34. Pfander D, Cramer T, Deuerling D, Weseloh G and Swoboda B: Expression of thrombospondin-1 and its receptor CD36 in human osteoarthritic cartilage. Ann Rheum Dis 59: 448-454, 2000.
35. Cecil DL, Appleton CT, Polewski MD, Mort JS, Schmidt AM, Bendele A, Beier F and Terkeltaub R: The pattern recognition receptor CD36 is a chondrocyte hypertrophy marker associated with suppression of catabolic responses and promotion of repair responses to infammatory stimuli. J Immunol 182: 5024-5031, 2009.
36. Zheng Q, Zhou G, Morello R, Chen Y, Garcia-Rojas X and Lee B: Type X collagen gene regulation by Runx2 contributes directly to its hypertrophic chondrocyte-specifc expression in vivo. J Cell Biol 162: 833-842, 2003.
37. Lin AC, Seeto BL, Bartoszko JM, Khoury MA, Whetstone H, Ho L, Hsu C, Ali SA and Alman BA: Modulating hedgehog signaling can attenuate the severity of osteoarthritis. Nat Med 15: 1421-1425, 2009.
38. Komori T: Regulation of bone development and extracellular matrix protein genes by RUNX2. Cell Tissue Res 339: 189-195, 2010.
39. Jin SY, Hong SJ, Yang HI, Park SD, Yoo MC, Lee HJ, Hong MS, Park HJ, Yoon SH, Kim BS, et al: Estrogen receptor-alpha gene haplotype is associated with primary knee osteoarthritis in Korean population. Arthritis Res Ther 6: R415-R421, 2004.
40. Lamas JR, Rodríguez-Rodríguez L, Vigo AG, Alvarez-Lafuente R, López-Romero P, Marco F, Camafeita E, Dopazo A, Callejas S, Villafuertes E, et al: Large-scale gene expression in bone marrow mesenchymal stem cells: A putative role for COL10A1 in osteoarthritis. Ann Rheum Dis 69: 1880-1885, 2010.