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
Experimental and Therapeutic Medicine
Join Editorial Board Propose a Special Issue
Print ISSN: 1792-0981 Online ISSN: 1792-1015
Journal Cover
July-2018 Volume 16 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-2018 Volume 16 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 Open Access

Identification of differential modules in ankylosing spondylitis using systemic module inference and the attract method

  • Authors:
    • Fang‑Chang Yuan
    • Bo Li
    • Li‑Jun Zhang
  • View Affiliations / Copyright

    Affiliations: Department of Orthopedics, People's Hospital of Rizhao, Rizhao, Shandong 276826, P.R. China, Department of Joint Surgery, Hospital of Xinjiang Production and Construction Corps, Urumchi, Xinjiang Uygur Autonomous Region 830002, P.R. China, Department of Orthopedics, The Fifth People's Hospital of Jinan, Jinan, Shandong 250022, P.R. China
    Copyright: © Yuan et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 149-154
    |
    Published online on: May 7, 2018
       https://doi.org/10.3892/etm.2018.6134
  • 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 objective of the present study was to identify differential modules in ankylosing spondylitis (AS) by integrating network analysis, module inference and the attract method. To achieve this objective, four steps were conducted. The first step was disease objective network (DON) for AS, and healthy objective network (HON) inference dependent on gene expression data, protein‑protein interaction networks and Spearman's correlation coefficient. In the second step, module detection was performed by utilizing a clique‑merging algorithm, which comprised of exploring maximal cliques by clique algorithm and refining or merging maximal cliques with a high overlap. The third part was seed module evaluation through module pair matches by Jaccard score and module correlation density (MCD) calculation. Finally, in the fourth step, differential modules between the AS and healthy groups were identified based on a gene set enrichment analysis‑analysis of variance model in the attract method. There were 5,301 nodes and 28,176 interactions both in DON and HON. A total of 20 and 21 modules were detected for the AS and healthy group, respectively. Notably, six seed modules across two groups were identified with Jaccard score ≥0.5, and these were ranked in descending order of differential MCD (ΔC). Seed module 1 had the highest ΔC of 0.077 and Jaccard score of 1.000. By accessing the attract method, one differential module between the AS group and healthy group was identified. In conclusion, the present study successfully identified one differential module for AS that may be a potential marker for AS target therapy and provide insights for future research on this disease.
View Figures

Figure 1

Figure 2

Figure 3

View References

1 

Chen J and Liu C: Sulfasalazine for ankylosing spondylitis. Cochrane Database Syst Rev: CD004800. 2005. View Article : Google Scholar

2 

Bleil J, Maier R, Hempfing A, Schlichting U, Appel H, Sieper J and Syrbe U: Histomorphologic and histomorphometric characteristics of zygapophyseal joint remodeling in ankylosing spondylitis. Arthritis Rheumatol. 66:1745–1754. 2014. View Article : Google Scholar : PubMed/NCBI

3 

Sykes M, Doll H and Gaffney K: Comment on: ‘Diagnostic delay in patients with rheumatoid arthritis, psoriatic arthritis and ankylosing spondylitis: Results from the Danish nationwide DANBIO registry’ by Sørensen et al. Ann Rheum Dis. 73:e442014. View Article : Google Scholar : PubMed/NCBI

4 

Brown MA, Kenna T and Wordsworth BP: Genetics of ankylosing spondylitis-insights into pathogenesis. Nat Rev Rheumatol. 12:81–91. 2016. View Article : Google Scholar : PubMed/NCBI

5 

Colbert RA, Tran TM and Layh-Schmitt G: HLA-B27 misfolding and ankylosing spondylitis. Mol Immunol. 57:44–51. 2014. View Article : Google Scholar : PubMed/NCBI

6 

Lin TT, Lu J, Qi CY, Yuan L, Li XL, Xia LP and Shen H: Elevated serum level of IL-27 and VEGF in patients with ankylosing spondylitis and associate with disease activity. Clin Exp Med. 15:227–231. 2015. View Article : Google Scholar : PubMed/NCBI

7 

Corr M: Wnt signaling in ankylosing spondylitis. Clin Rheumatol. 33:759–762. 2014. View Article : Google Scholar : PubMed/NCBI

8 

Nibbe RK, Chowdhury SA, Koyutürk M, Ewing R and Chance MR: Protein-protein interaction networks and subnetworks in the biology of disease. Wiley Interdiscip Rev Syst Biol Med. 3:357–367. 2011. View Article : Google Scholar : PubMed/NCBI

9 

Wu Y, Jing R, Jiang L, Jiang Y, Kuang Q, Ye L, Yang L, Li Y and Li M: Combination use of protein-protein interaction network topological features improves the predictive scores of deleterious non-synonymous single-nucleotide polymorphisms. Amino Acids. 46:2025–2035. 2014. View Article : Google Scholar : PubMed/NCBI

10 

Mar JC, Matigian NA, Quackenbush J and Wells CA: Attract: A method for identifying core pathways that define cellular phenotypes. PLoS One. 6:e254452011. View Article : Google Scholar : PubMed/NCBI

11 

Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B and Speed TP: Summaries of affymetrix GeneChip probe level data. Nucleic Acids Res. 31:e152003. View Article : Google Scholar : PubMed/NCBI

12 

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

13 

Bolstad B: affy: Built-in processing methods. 2013.

14 

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, et al: STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37:(Database Issue). D412–D416. 2009. View Article : Google Scholar : PubMed/NCBI

15 

Szmidt E and Kacprzyk J: The spearman rank correlation coefficient between intuitionistic fuzzy setsIEEE international conference on intelligent systems, is 2010. 7–9–July. 2010, University of Westminster; London: pp. 276–280, 2010. View Article : Google Scholar

16 

Liu G, Wong L and Chua HN: Complex discovery from weighted PPI networks. Bioinformatics. 25:1891–1897. 2009. View Article : Google Scholar : PubMed/NCBI

17 

Srihari S and Leong HW: A survey of computational methods for protein complex prediction from protein interaction networks. J Bioinform Comput Biol. 11:12300022013. View Article : Google Scholar : PubMed/NCBI

18 

Tomita E, Tanaka A and Takahashi H: The worst-case time complexity for generating all maximal cliques and computational experiments. Theoretical Computer Sci. 363:28–42. 2006. View Article : Google Scholar

19 

Sriganesh S and Ragan MA: Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics. 29:1553–1561. 2013. View Article : Google Scholar : PubMed/NCBI

20 

Srihari S and Ragan MA: Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics. 29:1553–1561. 2013. View Article : Google Scholar : PubMed/NCBI

21 

Bouchard M, Jousselme AL and Doré PE: A proof for the positive definiteness of the Jaccard index matrix. Int J Approximate Reasoning. 54:615–626. 2013. View Article : Google Scholar

22 

Gabow HN: An efficient implementation of Edmonds' algorithm for maximum matching on graphs. J ACM (JACM). 23:221–234. 1976. View Article : Google Scholar

23 

Mar J: 2011.attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape. Package version 1.18.0.

24 

Benjamini Y and Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Statistical Soc Series B (Methodological). 10:289–300. 1995.

25 

Göhre V and Robatzek S: Breaking the barriers: Microbial effector molecules subvert plant immunity. Annu Rev Phytopathol. 46:189–215. 2008. View Article : Google Scholar : PubMed/NCBI

26 

Ein-Dor L, Kela I, Getz G, Givol D and Domany E: Outcome signature genes in breast cancer: Is there a unique set? Bioinformatics. 21:171–178. 2005. View Article : Google Scholar : PubMed/NCBI

27 

Zhang L, Li S, Hao C, Hong G, Zou J, Zhang Y, Li P and Guo Z: Extracting a few functionally reproducible biomarkers to build robust subnetwork-based classifiers for the diagnosis of cancer. Gene. 526:232–238. 2013. View Article : Google Scholar : PubMed/NCBI

28 

Wu X, Zhao SH, Yu M, Zhu ZM, Wang H, Wang HL and Li K: Physical mapping of four porcine 20S proteasome core complex genes (PSMA1, PSMA2, PSMA3 and PSMA6). Cytogenet Genome Res. 108:3632005. View Article : Google Scholar

29 

Wright C, Edelmann M, diGleria K, Kollnberger S, Kramer H, McGowan S, McHugh K, Taylor S, Kessler B and Bowness P: Ankylosing spondylitis monocytes show upregulation of proteins involved in inflammation and the ubiquitin proteasome pathway. Ann Rheum Dis. 68:1626–1632. 2009. View Article : Google Scholar : PubMed/NCBI

30 

Wang GC, Zhao MJ and Wu DH: The expression of proteasome gene in the patients with ankylosing spondylitis. Chin J Rheumatol. 2003.(In Chinese).

31 

Kireva T, Polzer K, Neubert K, Meister S, Frey B, Baum W, Distler JH, Schett G, Voll RE and Zwerina J: Proteasome inhibition aggravates tumour necrosis factor-mediated bone resorption. Annals Rheumatic Dis. 69:61–75. 2010. View Article : Google Scholar

32 

Zhao H, Wang D, Fu D and Xue L: Predicting the potential ankylosing spondylitis-related genes utilizing bioinformatics approaches. Rheumatol Int. 35:973–979. 2015. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Yuan FC, Li B and Zhang LJ: Identification of differential modules in ankylosing spondylitis using systemic module inference and the attract method. Exp Ther Med 16: 149-154, 2018.
APA
Yuan, F., Li, B., & Zhang, L. (2018). Identification of differential modules in ankylosing spondylitis using systemic module inference and the attract method. Experimental and Therapeutic Medicine, 16, 149-154. https://doi.org/10.3892/etm.2018.6134
MLA
Yuan, F., Li, B., Zhang, L."Identification of differential modules in ankylosing spondylitis using systemic module inference and the attract method". Experimental and Therapeutic Medicine 16.1 (2018): 149-154.
Chicago
Yuan, F., Li, B., Zhang, L."Identification of differential modules in ankylosing spondylitis using systemic module inference and the attract method". Experimental and Therapeutic Medicine 16, no. 1 (2018): 149-154. https://doi.org/10.3892/etm.2018.6134
Copy and paste a formatted citation
x
Spandidos Publications style
Yuan FC, Li B and Zhang LJ: Identification of differential modules in ankylosing spondylitis using systemic module inference and the attract method. Exp Ther Med 16: 149-154, 2018.
APA
Yuan, F., Li, B., & Zhang, L. (2018). Identification of differential modules in ankylosing spondylitis using systemic module inference and the attract method. Experimental and Therapeutic Medicine, 16, 149-154. https://doi.org/10.3892/etm.2018.6134
MLA
Yuan, F., Li, B., Zhang, L."Identification of differential modules in ankylosing spondylitis using systemic module inference and the attract method". Experimental and Therapeutic Medicine 16.1 (2018): 149-154.
Chicago
Yuan, F., Li, B., Zhang, L."Identification of differential modules in ankylosing spondylitis using systemic module inference and the attract method". Experimental and Therapeutic Medicine 16, no. 1 (2018): 149-154. https://doi.org/10.3892/etm.2018.6134
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