Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Oncology Letters
      • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Biomedical Reports
      • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • Information for Authors
    • Information for Reviewers
    • Information for Librarians
    • Information for Advertisers
    • Conferences
  • Language Editing
Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • For Authors
    • For Reviewers
    • For Librarians
    • For Advertisers
    • Conferences
  • Language Editing
Login Register Submit
  • This site uses cookies
  • You can change your cookie settings at any time by following the instructions in our Cookie Policy. To find out more, you may read our Privacy Policy.

    I agree
Search articles by DOI, keyword, author or affiliation
Search
Advanced Search
presentation
Molecular Medicine Reports
Join Editorial Board Propose a Special Issue
Print ISSN: 1791-2997 Online ISSN: 1791-3004
Journal Cover
July-2014 Volume 10 Issue 1

Full Size Image

Sign up for eToc alerts
Recommend to Library

Journals

International Journal of Molecular Medicine

International Journal of Molecular Medicine

International Journal of Molecular Medicine is an international journal devoted to molecular mechanisms of human disease.

International Journal of Oncology

International Journal of Oncology

International Journal of Oncology is an international journal devoted to oncology research and cancer treatment.

Molecular Medicine Reports

Molecular Medicine Reports

Covers molecular medicine topics such as pharmacology, pathology, genetics, neuroscience, infectious diseases, molecular cardiology, and molecular surgery.

Oncology Reports

Oncology Reports

Oncology Reports is an international journal devoted to fundamental and applied research in Oncology.

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine is an international journal devoted to laboratory and clinical medicine.

Oncology Letters

Oncology Letters

Oncology Letters is an international journal devoted to Experimental and Clinical Oncology.

Biomedical Reports

Biomedical Reports

Explores a wide range of biological and medical fields, including pharmacology, genetics, microbiology, neuroscience, and molecular cardiology.

Molecular and Clinical Oncology

Molecular and Clinical Oncology

International journal addressing all aspects of oncology research, from tumorigenesis and oncogenes to chemotherapy and metastasis.

World Academy of Sciences Journal

World Academy of Sciences Journal

Multidisciplinary open-access journal spanning biochemistry, genetics, neuroscience, environmental health, and synthetic biology.

International Journal of Functional Nutrition

International Journal of Functional Nutrition

Open-access journal combining biochemistry, pharmacology, immunology, and genetics to advance health through functional nutrition.

International Journal of Epigenetics

International Journal of Epigenetics

Publishes open-access research on using epigenetics to advance understanding and treatment of human disease.

Medicine International

Medicine International

An International Open Access Journal Devoted to General Medicine.

Journal Cover
July-2014 Volume 10 Issue 1

Full Size Image

Sign up for eToc alerts
Recommend to Library

  • Article
  • Citations
    • Cite This Article
    • Download Citation
    • Create Citation Alert
    • Remove Citation Alert
    • Cited By
  • Similar Articles
    • Related Articles (in Spandidos Publications)
    • Similar Articles (Google Scholar)
    • Similar Articles (PubMed)
  • Download PDF
  • Download XML
  • View XML
Article

Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co‑expression network

  • Authors:
    • Qing‑You Lu
    • Qing‑Hui Han
    • Xia Li
    • Zeng‑Chun Li
    • Yu‑Tao Pan
    • Lin Liu
    • Qing‑Ge Fu
  • View Affiliations / Copyright

    Affiliations: Department of Trauma Surgery, East Hospital Affiliated to Tongji University, Shanghai 200120, P.R. China
  • Pages: 119-124
    |
    Published online on: April 24, 2014
       https://doi.org/10.3892/mmr.2014.2166
  • Expand metrics +
Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )
Cited By (CrossRef): 0 citations Loading Articles...

This article is mentioned in:



Abstract

The aim of the current study was to investigate disease‑associated genes and related molecular mechanisms of osteoarthritis (OA) and rheumatoid arthritis (RA). Using GSE7669 datasets downloaded from Gene Expression Omnibus databases, the differentially expressed genes (DEGs) between RA and OA synovial fibroblasts (SFBs) (n=6 each) were screened. DEG‑associated co‑expression and topological properties were analyzed to determine the rank of disease‑associated genes. Specifically, the fold change of differentially expressed genes, the clustering coefficient and the degree of differential gene co-expression were integrated to determine the disease‑associated gene ranking. The underlying molecular mechanisms of these crucial disease‑associated genes were investigated by gene ontology (GO) enrichment analysis. A total of 1313 DEGs, including 1068 upregulated genes and 245 downregulated genes were observed. The top 20 disease‑associated genes were identified, including proteoglycan 4, inhibin β B, carboxypeptidase M, alcohol dehydrogenase 1C and integrin β2. The major GO biological processes of these top 20 disease‑associated genes were highly involved in the immune system, such as responses to stimuli, immune responses and inflammatory responses. This large‑scale gene expression study observed disease‑associated genes and their associated GO function in RA and OA, which may provide opportunities for biomarker development and novel insights into the molecular mechanisms of these two diseases.
View Figures

Figure 1

Figure 2

Figure 3

View References

1 

Maini R, Plater-Zyberk C and Andrew E: Autoimmunity in rheumatoid arthritis. An approach via a study of B lymphocytes. Rheum Dis Clin North Am. 13:319–338. 1987.PubMed/NCBI

2 

Buckwalter J and Mankin H: Articular cartilage: degeneration and osteoarthritis, repair, regeneration, and transplantation. Instr Course Lect. 47:487–504. 1997.PubMed/NCBI

3 

Brown RA and Weiss JB: Neovascularisation and its role in the osteoarthritic process. Ann Rheum Dis. 47:881–885. 1988. View Article : Google Scholar : PubMed/NCBI

4 

Sattar A, Kumar P and Kumar S: Rheumatoid- and osteo-arthritis: quantitation of ultrastructural features of capillary endothelial cells. J Pathol. 148:45–53. 1986. View Article : Google Scholar : PubMed/NCBI

5 

Keyszer G, Redlich A, Häupl T, et al: Differential expression of cathepsins B and L compared with matrix metalloproteinases and their respective inhibitors in rheumatoid arthritis and osteoarthritis: a parallel investigation by semiquantitative reverse transcriptase-polymerase chain reaction and immunohistochemistry. Arthritis Rheum. 41:1378–1387. 1998.

6 

Ayral X, Pickering E, Woodworth T, Mackillop N and Dougados M: Synovitis: a potential predictive factor of structural progression of medial tibiofemoral knee osteoarthritis - results of a 1 year longitudinal arthroscopic study in 422 patients. Osteoarthritis Cartilage. 13:361–367. 2005.

7 

Emery P, Breedveld FUC, Lemmel EM, et al: A comparison of the efficacy and safety of leflunomide and methotrexate for the treatment of rheumatoid arthritis. Rheumatology (Oxford). 39:655–665. 2000. View Article : Google Scholar : PubMed/NCBI

8 

Superio-Cabuslay E, Ward MM and Lorig KR: Patient education interventions in osteoarthritis and rheumatoid arthritis: a meta-analytic comparison with nonsteroidal antiinflammatory drug treatment. Arthritis Care Res. 9:292–301. 1996. View Article : Google Scholar

9 

Ross C: A comparison of osteoarthritis and rheumatoid arthritis: diagnosis and treatment. Nurse Pract. 22:20–41. 1997. View Article : Google Scholar : PubMed/NCBI

10 

Kofoed H and Sørensen TS: Ankle arthroplasty for rheumatoid arthritis and osteoarthritis: prospective long-term study of cemented replacements. J Bone Joint Surg Br. 80:328–332. 1998. View Article : Google Scholar : PubMed/NCBI

11 

Wajon A, Carr E, Edmunds I and Ada L: Surgery for thumb (trapeziometacarpal joint) osteoarthritis. Cochrane Database Syst Rev. Oct 7;CD0046312009.

12 

Silverstein FE, Faich G, Goldstein JL, et al: Gastrointestinal toxicity with celecoxib vs nonsteroidal anti-inflammatory drugs for osteoarthritis and rheumatoid arthritis: the CLASS study: a randomized controlled trial. Celecoxib Long-term Arthritis Safety Study. JAMA. 284:1247–1255. 2000. View Article : Google Scholar

13 

Deeks JJ, Smith LA and Bradley MD: Efficacy, tolerability, and upper gastrointestinal safety of celecoxib for treatment of osteoarthritis and rheumatoid arthritis: systematic review of randomised controlled trials. BMJ. 325:6192002. View Article : Google Scholar

14 

Bramlage CP, Häupl T, Kaps C, et al: Decrease in expression of bone morphogenetic proteins 4 and 5 in synovial tissue of patients with osteoarthritis and rheumatoid arthritis. Arthritis Res Ther. 8:R582006. View Article : Google Scholar : PubMed/NCBI

15 

Pohlers D, Beyer A, Koczan D, Wilhelm T, Thiesen HJ and Kinne RW: Constitutive upregulation of the transforming growth factor-beta pathway in rheumatoid arthritis synovial fibroblasts. Arthritis Res Ther. 9:R592007. View Article : Google Scholar : PubMed/NCBI

16 

Bolstad BM, Irizarry RA, Astrand M and Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 19:185–193. 2003. View Article : Google Scholar : PubMed/NCBI

17 

Tusher VG, Tibshirani R and Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA. 98:5116–5121. 2001. View Article : Google Scholar : PubMed/NCBI

18 

Shannon P, Markiel A, Ozier O, et al: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498–2504. 2003. View Article : Google Scholar : PubMed/NCBI

19 

Ruan J, Dean AK and Zhang W: A general co-expression network-based approach to gene expression analysis: comparison and applications. BMC Syst Biol. 4:82010. View Article : Google Scholar : PubMed/NCBI

20 

Tiret L, Rigat B, Visvikis S, et al: Evidence, from combined segregation and linkage analysis, that a variant of the angiotensin I-converting enzyme (ACE) gene controls plasma ACE levels. Am J Hum Genet. 51:197–205. 1992.PubMed/NCBI

21 

Schmitt WA Jr, Raab RM and Stephanopoulos G: Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data. Genome Res. 14:1654–1663. 2004. View Article : Google Scholar : PubMed/NCBI

22 

Welsh JB, Zarrinkar PP, Sapinoso LM, et al: Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci USA. 98:1176–1181. 2001. View Article : Google Scholar

23 

Huang da W, Sherman BT, Tan Q, et al: DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35:W169–W175. 2007.PubMed/NCBI

24 

Aoki-Kinoshita KF and Kanehisa M: Gene annotation and pathway mapping in KEGG. Methods Mol Biol. 396:71–91. 2007. View Article : Google Scholar : PubMed/NCBI

25 

Bucala R, Ritchlin C, Winchester R and Cerami A: Constitutive production of inflammatory and mitogenic cytokines by rheumatoid synovial fibroblasts. J Exp Med. 173:569–574. 1991. View Article : Google Scholar : PubMed/NCBI

26 

Schadt EE and Lum PY: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes. J Lipid Res. 47:2601–2613. 2006. View Article : Google Scholar

27 

Martin S, Richards AJ, Yates J, Scott JD, Pope M and Snead MP: Stickler syndrome: further mutations in COL11A1 and evidence for additional locus heterogeneity. Eur J Hum Genet. 7:807–814. 1999. View Article : Google Scholar : PubMed/NCBI

28 

Kahler RA, Yingst S, Hoeppner LH, et al: Collagen 11a1 is indirectly activated by lymphocyte enhancer-binding factor 1 (Lef1) and negatively regulates osteoblast maturation. Matrix Biol. 27:330–338. 2008. View Article : Google Scholar : PubMed/NCBI

29 

Meulenbelt I: Osteoarthritis year 2011 in review: genetics. Osteoarthritis Cartilage. 20:218–222. 2012.

30 

Ruan MZ, Erez A, Guse K, et al: Proteoglycan 4 expression protects against the development of osteoarthritis. Sci Transl Med. 5:176ra342013.PubMed/NCBI

31 

Rinaldi N, Schwarz-Eywill M, Weis D, et al: Increased expression of integrins on fibroblast-like synoviocytes from rheumatoid arthritis in vitro correlates with enhanced binding to extracellular matrix proteins. Ann Rheum Dis. 56:45–51. 1997. View Article : Google Scholar

32 

El-Gendi SS, Moniem AE, Tawfik NM, Ashmawy MM, Mohammed OA, Mostafa AK, Zakhari MM and Herdan OM: Value of serum and synovial fluid activin A and inhibin A in some rheumatic diseases. Int J Rheum Dis. 13:273–279. 2010. View Article : Google Scholar : PubMed/NCBI

33 

Scanzello CR, Plaas A and Crow MK: Innate immune system activation in osteoarthritis: is osteoarthritis a chronic wound? Curr Opin Rheum. 20:565–572. 2008. View Article : Google Scholar : PubMed/NCBI

34 

Sakkas LI and Platsoucas CD: The role of T cells in the pathogenesis of osteoarthritis. Arthritis Rheum. 56:409–424. 2007. View Article : Google Scholar : PubMed/NCBI

35 

Feldmann M and Maini RN; Lasker Clinical Medical Research Award. TNF defined as a therapeutic target for rheumatoid arthritis and other autoimmune diseases. Nat Med. 9:1245–1250. 2003. View Article : Google Scholar : PubMed/NCBI

36 

McInnes IB and Schett G: Cytokines in the pathogenesis of rheumatoid arthritis. Nat Rev Immunol. 7:429–442. 2007. View Article : Google Scholar : PubMed/NCBI

37 

Karatay S, Kiziltunc A, Yildirim K, Karanfil RC and Senel K: Effects of different hyaluronic acid products on synovial fluid levels of intercellular adhesion molecule-1 and vascular cell adhesion molecule-1 in knee osteoarthritis. Ann Clin Lab Sci. 34:330–335. 2004.PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Lu QY, Han QH, Li X, Li ZC, Pan YT, Liu L and Fu QG: Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co‑expression network. Mol Med Rep 10: 119-124, 2014.
APA
Lu, Q., Han, Q., Li, X., Li, Z., Pan, Y., Liu, L., & Fu, Q. (2014). Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co‑expression network. Molecular Medicine Reports, 10, 119-124. https://doi.org/10.3892/mmr.2014.2166
MLA
Lu, Q., Han, Q., Li, X., Li, Z., Pan, Y., Liu, L., Fu, Q."Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co‑expression network". Molecular Medicine Reports 10.1 (2014): 119-124.
Chicago
Lu, Q., Han, Q., Li, X., Li, Z., Pan, Y., Liu, L., Fu, Q."Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co‑expression network". Molecular Medicine Reports 10, no. 1 (2014): 119-124. https://doi.org/10.3892/mmr.2014.2166
Copy and paste a formatted citation
x
Spandidos Publications style
Lu QY, Han QH, Li X, Li ZC, Pan YT, Liu L and Fu QG: Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co‑expression network. Mol Med Rep 10: 119-124, 2014.
APA
Lu, Q., Han, Q., Li, X., Li, Z., Pan, Y., Liu, L., & Fu, Q. (2014). Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co‑expression network. Molecular Medicine Reports, 10, 119-124. https://doi.org/10.3892/mmr.2014.2166
MLA
Lu, Q., Han, Q., Li, X., Li, Z., Pan, Y., Liu, L., Fu, Q."Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co‑expression network". Molecular Medicine Reports 10.1 (2014): 119-124.
Chicago
Lu, Q., Han, Q., Li, X., Li, Z., Pan, Y., Liu, L., Fu, Q."Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co‑expression network". Molecular Medicine Reports 10, no. 1 (2014): 119-124. https://doi.org/10.3892/mmr.2014.2166
Follow us
  • Twitter
  • LinkedIn
  • Facebook
About
  • Spandidos Publications
  • Careers
  • Cookie Policy
  • Privacy Policy
How can we help?
  • Help
  • Live Chat
  • Contact
  • Email to our Support Team