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
April-2019 Volume 17 Issue 4

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
April-2019 Volume 17 Issue 4

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

Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology

  • Authors:
    • Wenjiu Yang
    • Jing Han
    • Jinfeng Ma
    • Yujie Feng
    • Qingxian Hou
    • Zhijie Wang
    • Tengbo Yu
  • View Affiliations / Copyright

    Affiliations: Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China, Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China, Department of Hepatobiliary Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China, Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China
    Copyright: © Yang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 2561-2566
    |
    Published online on: January 29, 2019
       https://doi.org/10.3892/etm.2019.7216
  • 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

Guilt by association (GBA) algorithm has been widely used to predict gene functions statistically, and a network-based approach may increase the confidence and veracity of identifying molecular signatures for diseases. The aim of the present study was to suggest a gene ontology (GO)-based method by integrating the GBA algorithm and network, to identify key gene functions for spinal muscular atrophy (SMA). The inference of predicting key gene functions was comprised of four steps, preparing gene lists and sets; extracting differentially expressed genes (DEGs) using microarray data [linear models for microarray data (limma)] package; constructing a co-expression matrix on gene lists using the Spearman correlation coefficient method; and predicting gene functions by GBA algorithm. Ultimately, key gene functions were predicted according to the area under the curve (AUC) index for GO terms and the GO terms with AUC >0.7 were determined as the optimal gene functions for SMA. A total of 484 DEGs and 466 background GO terms were regarded as gene lists and sets for the subsequent analyses, respectively. The predicted results obtained from the network-based GBA approach showed 141 gene sets had a good classified performance with AUC >0.5. Most significantly, 3 gene sets with AUC >0.7 were denoted as seed gene functions for SMA, including cell morphogenesis, which is involved in differentiation and ossification. In conclusion, we have predicted 3 key gene functions for SMA compared with control utilizing network-based GBA algorithm. The findings may provide great insights to reveal pathological and molecular mechanism underlying SMA.
View Figures

Figure 1

Figure 2

Figure 3

View References

1 

Nurputra DK, Lai PS, Harahap NI, Morikawa S, Yamamoto T, Nishimura N, Kubo Y, Takeuchi A, Saito T, Takeshima Y, et al: Spinal muscular atrophy: From gene discovery to clinical trials. Ann Hum Genet. 77:435–463. 2013. View Article : Google Scholar : PubMed/NCBI

2 

Grunseich C, Zukosky K, Kats IR, Ghosh L, Harmison GG, Bott LC, Rinaldi C, Chen KL, Chen G, Boehm M, et al: Stem cell-derived motor neurons from spinal and bulbar muscular atrophy patients. Neurobiol Dis. 70:12–20. 2014. View Article : Google Scholar : PubMed/NCBI

3 

Kirschner J, Schorling D, Hauschke D, Rensing-Zimmermann C, Wein U, Grieben U, Schottmann G, Schara U, Konrad K, Müller-Felber W, et al: Somatropin treatment of spinal muscular atrophy: A placebo-controlled, double-blind crossover pilot study. Neuromuscul Disord. 24:134–142. 2014. View Article : Google Scholar : PubMed/NCBI

4 

Gillis J and Pavlidis P: The impact of multifunctional genes on ‘guilt by association’ analysis. PLoS One. 6:e172582011. View Article : Google Scholar : PubMed/NCBI

5 

Gillis J and Pavlidis P: ‘Guilt by Association’ is the exception rather than the rule in gene networks. PLoS Comput Biol. 8:e10024442012. View Article : Google Scholar : PubMed/NCBI

6 

Zeng X, Liao Y, Liu Y and Zou Q: Prediction and validation of disease genes using HeteSim Scores. IEEE/ACM Trans Comput Biol Bioinformatics. 14:687–695. 2017. View Article : Google Scholar

7 

Wang S, Huang G, Hu Q and Zou Q: A network-based method for the identification of putative genes related to infertility. Biochim Biophys Acta 1860 (11 Pt B). 2716–2724. 2016.

8 

Molet M, Stagner JP, Miller HC, Kosinski T and Zentall TR: Guilt by association and honor by association: The role of acquired equivalence. Psychon Bull Rev. 20:385–390. 2013. View Article : Google Scholar : PubMed/NCBI

9 

Vey G: Metagenomic guilt by association: An operonic perspective. PLoS One. 8:e714842013. View Article : Google Scholar : PubMed/NCBI

10 

Mulcahy PJ, Iremonger K, Karyka E, Herranz-Martín S, Shum KT, Tam JK and Azzouz M: Gene therapy: A promising approach to treating spinal muscular atrophy. Hum Gene Ther. 25:575–586. 2014. View Article : Google Scholar : PubMed/NCBI

11 

Raleigh DP: Guilt by association: The physical chemistry and biology of protein aggregation. J Phys Chem Lett. 5:2012–2014. 2014. View Article : Google Scholar : PubMed/NCBI

12 

Verleyen W, Ballouz S and Gillis J: Measuring the wisdom of the crowds in network-based gene function inference. Bioinformatics. 31:745–752. 2014. View Article : Google Scholar : PubMed/NCBI

13 

Levy PD: Guilt by association - A closer look at calcium, heart failure, and mortality. J Card Fail. 21:628–629. 2015. View Article : Google Scholar : PubMed/NCBI

14 

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

15 

Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, et al: A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 15:1552014. View Article : Google Scholar : PubMed/NCBI

16 

Gene Ontology Consortium: Gene Ontology Consortium: Going forward. Nucleic Acids Res 43 (D1). D1049–D1056. 2015. View Article : Google Scholar

17 

Zou M, Liu Z, Zhang XS and Wang Y: NCC-AUC: An AUC optimization method to identify multibiomarker panel for cancer prognosis from genomic and clinical data. Bioinformatics. 15:3330–3338. 2015. View Article : Google Scholar

18 

Gillis J and Pavlidis P: The role of indirect connections in gene networks in predicting function. Bioinformatics. 27:1860–1866. 2011. View Article : Google Scholar : PubMed/NCBI

19 

Willson DF: Outcomes and risk factors in pediatric ventilator-associated pneumonia: Guilt by association. Pediatr Crit Care Med. 16:299–301. 2015. View Article : Google Scholar : PubMed/NCBI

20 

Becker D, Otto M, Ammann P, Keller I, Drögemüller C and Leeb T: The brown coat colour of Coppernecked goats is associated with a non-synonymous variant at the TYRP1 locus on chromosome 8. Anim Genet. 46:50–54. 2015. View Article : Google Scholar : PubMed/NCBI

21 

Rousseau B, Larrieu-Lahargue F, Javerzat S, Guilhem-Ducléon F, Beermann F and Bikfalvi A: The tyrp1-Tag/tyrp1-FGFR1-DN bigenic mouse: a model for selective inhibition of tumor development, angiogenesis, and invasion into the neural tissue by blockade of fibroblast growth factor receptor activity. Cancer Res. 64:2490–2495. 2004. View Article : Google Scholar : PubMed/NCBI

22 

Veiga-da-Cunha M, Hadi F, Balligand T, Stroobant V and Van Schaftingen E: Molecular identification of hydroxylysine kinase and of ammoniophospholyases acting on 5-phosphohydroxy-L-lysine and phosphoethanolamine. J Biol Chem. 287:7246–7255. 2012. View Article : Google Scholar : PubMed/NCBI

23 

Vives-Rodriguez A, Sivaraju A and Louis ED: Drop attacks: A clinical manifestation of LGI1 encephalitis. Neurol Clin Pract. 7:442–443. 2017. View Article : Google Scholar : PubMed/NCBI

24 

Nikolaus M, Jackowski-Dohrmann S, Prüss H, Schuelke M and Knierim E: Morvan syndrome associated with CASPR2 and LGI1 antibodies in a child. Neurology. 90:183–185. 2018. View Article : Google Scholar : PubMed/NCBI

25 

Chen Y, Huang Q, Zhou H, Wang Y, Hu X and Li T: Inhibition of canonical WNT/β-catenin signaling is involved in leflunomide (LEF)-mediated cytotoxic effects on renal carcinoma cells. Oncotarget. 7:50401–50416. 2016.PubMed/NCBI

26 

Chen Z, Gao Y, Yao L, Liu Y, Huang L, Yan Z, Zhao W, Zhu P and Weng H: LncFZD6 initiates Wnt/β-catenin and liver TIC self-renewal through BRG1-mediated FZD6 transcriptional activation. Oncogene. 37:3098–3112. 2018. View Article : Google Scholar : PubMed/NCBI

27 

Wan Y, Rogers MB and Szabo-Rogers HL: A six-gene expression toolbox for the glands, epithelium and chondrocytes in the mouse nasal cavity. Gene Expr Patterns. 27:46–55. 2018. View Article : Google Scholar : PubMed/NCBI

28 

Cui S, Zhang W, Xiong L, Pan F, Niu Y, Chu T, Wang H, Zhao Y and Jiang L: Use of capture-based next-generation sequencing to detect ALK fusion in plasma cell-free DNA of patients with non-small-cell lung cancer. Oncotarget. 8:2771–2780. 2017.PubMed/NCBI

29 

Shojaati G, Khandaker I, Sylakowski K, Funderburgh ML, Du Y and Funderburgh JL: Compressed collagen enhances stem cell therapy for corneal scarring. Stem Cells Transl Med. 7:487–494. 2018. View Article : Google Scholar : PubMed/NCBI

30 

Drilon A, Somwar R, Mangatt BP, Edgren H, Desmeules P, Ruusulehto A, Smith RS, Delasos L, Vojnic M, Plodkowski AJ, et al: Response to ERBB3-directed targeted therapy in NRG1-rearranged cancers. Cancer Discov. 8:686–695. 2018. View Article : Google Scholar : PubMed/NCBI

31 

Varner VD and Nelson CM: Cellular and physical mechanisms of branching morphogenesis. Development. 141:2750–2759. 2014. View Article : Google Scholar : PubMed/NCBI

32 

Wu M and Li J: Numb family proteins: Novel players in cardiac morphogenesis and cardiac progenitor cell differentiation. Biomol Concepts. 6:137–148. 2015. View Article : Google Scholar : PubMed/NCBI

33 

Kolb SJ and Kissel JT: Spinal muscular atrophy. Neurol Clin. 33:831–846. 2015. View Article : Google Scholar : PubMed/NCBI

34 

Anderton RS and Mastaglia FL: Advances and challenges in developing a therapy for spinal muscular atrophy. Expert Rev Neurother. 15:895–908. 2015.PubMed/NCBI

35 

Takahashi K, Satoh M, Takahashi Y, Osaki T, Nasu T, Tamada M, Okabayashi H, Nakamura M and Morino Y: Dysregulation of ossification-related miRNAs in circulating osteogenic progenitor cells obtained from patients with aortic stenosis. Clin Sci (Lond). 130:1115–1124. 2016. View Article : Google Scholar : PubMed/NCBI

36 

Li J, Jiang D, Zhou H, Li F, Yang J, Hong L, Fu X, Li Z, Liu Z, Li J, et al: Expression of RNA-interference/antisense transgenes by the cognate promoters of target genes is a better gene-silencing strategy to study gene functions in rice. PLoS One. 6:e174442011. View Article : Google Scholar : PubMed/NCBI

37 

Klie S, Nikoloski Z and Selbig J: Biological cluster evaluation for gene function prediction. J Comput Biol. 21:428–445. 2014. View Article : Google Scholar : PubMed/NCBI

38 

Zanetta C, Nizzardo M, Simone C, Monguzzi E, Bresolin N, Comi GP and Corti S: Molecular therapeutic strategies for spinal muscular atrophies: Current and future clinical trials. Clin Ther. 36:128–140. 2014. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Yang W, Han J, Ma J, Feng Y, Hou Q, Wang Z and Yu T: Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology. Exp Ther Med 17: 2561-2566, 2019.
APA
Yang, W., Han, J., Ma, J., Feng, Y., Hou, Q., Wang, Z., & Yu, T. (2019). Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology. Experimental and Therapeutic Medicine, 17, 2561-2566. https://doi.org/10.3892/etm.2019.7216
MLA
Yang, W., Han, J., Ma, J., Feng, Y., Hou, Q., Wang, Z., Yu, T."Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology". Experimental and Therapeutic Medicine 17.4 (2019): 2561-2566.
Chicago
Yang, W., Han, J., Ma, J., Feng, Y., Hou, Q., Wang, Z., Yu, T."Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology". Experimental and Therapeutic Medicine 17, no. 4 (2019): 2561-2566. https://doi.org/10.3892/etm.2019.7216
Copy and paste a formatted citation
x
Spandidos Publications style
Yang W, Han J, Ma J, Feng Y, Hou Q, Wang Z and Yu T: Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology. Exp Ther Med 17: 2561-2566, 2019.
APA
Yang, W., Han, J., Ma, J., Feng, Y., Hou, Q., Wang, Z., & Yu, T. (2019). Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology. Experimental and Therapeutic Medicine, 17, 2561-2566. https://doi.org/10.3892/etm.2019.7216
MLA
Yang, W., Han, J., Ma, J., Feng, Y., Hou, Q., Wang, Z., Yu, T."Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology". Experimental and Therapeutic Medicine 17.4 (2019): 2561-2566.
Chicago
Yang, W., Han, J., Ma, J., Feng, Y., Hou, Q., Wang, Z., Yu, T."Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology". Experimental and Therapeutic Medicine 17, no. 4 (2019): 2561-2566. https://doi.org/10.3892/etm.2019.7216
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