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
January-2019 Volume 17 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
January-2019 Volume 17 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

Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma

  • Authors:
    • Meng Yang
    • Qi Wan
    • Xiang Hu
    • Haitao Yin
    • Dawei Hao
    • Chengjun Wu
    • Jianmin Li
  • View Affiliations / Copyright

    Affiliations: Department of Dermatology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530031, P.R. China, Department of Ophthalmology, The People's Hospital of Leshan, Leshan, Sichuan 614000, P.R. China, Department of Radiotherapy, Xuzhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Xuzhou, Jiangsu 221009, P.R. China
    Copyright: © Yang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 237-243
    |
    Published online on: November 9, 2018
       https://doi.org/10.3892/etm.2018.6945
  • 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

Uveal melanoma (UM) is a tumor that affects individuals throughout the world. Although gene expression analysis of UM has been performed previously, systemic co‑expression analysis for this type of cancer remains lacking. Microarray data of UM samples was obtained from the Genome Expression Omnibus (dataset GSE44295). Co‑expression modules were built by weighted gene co‑expression network analysis. Functional enrichment analysis was performed on the co‑expressed genes from important modules. Seven co‑expression modules were constructed from the 5,000 genes gathered from the 58 human UM samples. The number of genes in these modules ranged from 73 to 3,051, with the mean number being 711. There was a marked difference in interactions among pairwise modules. Functional enrichment analysis demonstrated that module 2 was mainly enriched in pathways associated with the regulation of transcription. Additionally, modules 2‑4 were significantly enriched in the ubiquitin mediated proteolysis pathway, suggesting it could serve a critical role in the occurrence and development of UM. The findings of the present study present a framework of co‑expressed gene modules for human UM and provide an improved understanding of these modules at a functional level. Understanding the molecular mechanism and cellular pathways involved in pathogenesis of UM is extremely important for the development of more effective diagnostic and therapeutic strategies.
View Figures

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

View References

1 

Stang A, Parkin DM, Ferlay J and Jöckel KH: International uveal melanoma incidence trends in view of a decreasing proportion of morphological verification. Int J Cancer. 114:114–123. 2005. View Article : Google Scholar : PubMed/NCBI

2 

Singh AD and Topham A: Incidence of uveal melanoma in the United States: 1973–1997. Ophthalmology. 110:956–961. 2003. View Article : Google Scholar : PubMed/NCBI

3 

Egan KM, Seddon JM, Glynn RJ, Gragoudas ES and Albert DM: Epidemiologic aspects of uveal melanoma. Surv Ophthalmol. 32:239–251. 1988. View Article : Google Scholar : PubMed/NCBI

4 

Bedikian AY, Legha SS, Mavligit G, Carrasco CH, Khorana S, Plager C, Papadopoulos N and Benjamin RS: Treatment of uveal melanoma metastatic to the liver: A review of the M.D. Anderson Cancer Center experience and prognostic factors. Cancer. 76:1665–1670. 1995. View Article : Google Scholar : PubMed/NCBI

5 

Clarke C, Madden SF, Doolan P, Aherne ST, Joyce H, O'Driscoll L, Gallagher WM, Hennessy BT, Moriarty M, Crown J, et al: Correlating transcriptional networks to breast cancer survival: A large-scale coexpression analysis. Carcinogenesis. 34:2300–2308. 2013. View Article : Google Scholar : PubMed/NCBI

6 

Wan Q, Tang J, Han Y and Wang D: Co-expression modules construction by WGCNA and identify potential prognostic markers of uveal melanoma. Exp Eye Res. 166:13–20. 2018. View Article : Google Scholar : PubMed/NCBI

7 

Langfelder P and Horvath S: WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics. 9:5592008. View Article : Google Scholar : PubMed/NCBI

8 

Shi Z, Derow CK and Zhang B: Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. BMC Syst Biol. 4:742010. View Article : Google Scholar : PubMed/NCBI

9 

Udyavar AR, Hoeksema MD, Clark JE, Zou Y, Tang Z, Li Z, Li M, Chen H, Statnikov A, Shyr Y, et al: Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer. BMC Syst Biol. 7 Suppl 5:S12013. View Article : Google Scholar : PubMed/NCBI

10 

Ihaka R and Gentleman R: R: A language for data analysis and graphics. J Comput Graph Stat. 5:299–314. 1996. View Article : Google Scholar

11 

Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC and Lempicki RA: DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol. 4:P32003. View Article : Google Scholar : PubMed/NCBI

12 

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al: Gene ontology: Tool for the unification of biology. Nat Genet. 25:25–29. 2000. View Article : Google Scholar : PubMed/NCBI

13 

Kanehisa M, Goto S, Kawashima S, Okuno Y and Hattori M: The KEGG resource for deciphering the genome. Nucleic Acids Res. 32:(Database Issue). D277–D280. 2004. View Article : Google Scholar : PubMed/NCBI

14 

Kanehisa M and Goto S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27–30. 2000. View Article : Google Scholar : PubMed/NCBI

15 

Gong J, Cao J, Liu G and Huo JR: Function and mechanism of F-box proteins in gastric cancer (Review). Int J Oncol. 47:43–50. 2015. View Article : Google Scholar : PubMed/NCBI

16 

Testa U: Proteasome inhibitors in cancer therapy. Curr Drug Targets. 10:968–981. 2009. View Article : Google Scholar : PubMed/NCBI

17 

Sane S and Rezvani K: Essential roles of E3 ubiquitin ligases in p53 regulation. Int J Mol Sci. 18:E4422017. View Article : Google Scholar : PubMed/NCBI

18 

Weathington NM and Mallampalli RK: Emerging therapies targeting the ubiquitin proteasome system in cancer. J Clin Invest. 124:6–12. 2014. View Article : Google Scholar : PubMed/NCBI

19 

Liu J, Shaik S, Dai X, Wu Q, Zhou X, Wang Z and Wei W: Targeting the ubiquitin pathway for cancer treatment. Biochim Biophys Acta. 1855:50–60. 2015.PubMed/NCBI

20 

Gragoudas ES, Egan KM, Seddon JM, Glynn RJ, Walsh SM, Finn SM, Munzenrider JE and Spar MD: Survival of patents with metastases from uveal melanoma. Ophthalmology. 98:383–390. 1991. View Article : Google Scholar : PubMed/NCBI

21 

Harbour JW, Onken MD, Roberson ED, Duan S, Cao L, Worley LA, Council ML, Matatall KA, Helms C and Bowcock AM: Frequent mutation of BAP1 in metastasizing uveal melanomas. Science. 330:1410–1413. 2010. View Article : Google Scholar : PubMed/NCBI

22 

Woodman SE: Metastatic uveal melanoma: Biology and emerging treatments. Cancer J. 18:148–152. 2012. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Yang M, Wan Q, Hu X, Yin H, Hao D, Wu C and Li J: Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma. Exp Ther Med 17: 237-243, 2019.
APA
Yang, M., Wan, Q., Hu, X., Yin, H., Hao, D., Wu, C., & Li, J. (2019). Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma. Experimental and Therapeutic Medicine, 17, 237-243. https://doi.org/10.3892/etm.2018.6945
MLA
Yang, M., Wan, Q., Hu, X., Yin, H., Hao, D., Wu, C., Li, J."Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma". Experimental and Therapeutic Medicine 17.1 (2019): 237-243.
Chicago
Yang, M., Wan, Q., Hu, X., Yin, H., Hao, D., Wu, C., Li, J."Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma". Experimental and Therapeutic Medicine 17, no. 1 (2019): 237-243. https://doi.org/10.3892/etm.2018.6945
Copy and paste a formatted citation
x
Spandidos Publications style
Yang M, Wan Q, Hu X, Yin H, Hao D, Wu C and Li J: Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma. Exp Ther Med 17: 237-243, 2019.
APA
Yang, M., Wan, Q., Hu, X., Yin, H., Hao, D., Wu, C., & Li, J. (2019). Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma. Experimental and Therapeutic Medicine, 17, 237-243. https://doi.org/10.3892/etm.2018.6945
MLA
Yang, M., Wan, Q., Hu, X., Yin, H., Hao, D., Wu, C., Li, J."Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma". Experimental and Therapeutic Medicine 17.1 (2019): 237-243.
Chicago
Yang, M., Wan, Q., Hu, X., Yin, H., Hao, D., Wu, C., Li, J."Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma". Experimental and Therapeutic Medicine 17, no. 1 (2019): 237-243. https://doi.org/10.3892/etm.2018.6945
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