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Identification of hub subnetwork based on topological features of genes in breast cancer

  • Authors:
    • Da-Yong Zhuang
    • Li Jiang
    • Qing-Qing He
    • Peng Zhou
    • Tao Yue
  • View Affiliations / Copyright

    Affiliations: Department of Thyroid and Breast Surgery, Jinan Military General Hospital of Chinese PLA, Jinan, Shandong 250031, P.R. China, Department of Prevention and Health Care, Central Hospital of Zibo City, Zibo, Shandong 255036, P.R. China
    Copyright: © Zhuang et al. This is an open access article distributed under the terms of Creative Commons Attribution License [CC BY_NC 3.0].
  • Pages: 664-674
    |
    Published online on: December 30, 2014
       https://doi.org/10.3892/ijmm.2014.2057
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Abstract

The aim of this study was to provide functional insight into the identification of hub subnetworks by aggregating the behavior of genes connected in a protein-protein interaction (PPI) network. We applied a protein network-based approach to identify subnetworks which may provide new insight into the functions of pathways involved in breast cancer rather than individual genes. Five groups of breast cancer data were downloaded and analyzed from the Gene Expression Omnibus (GEO) database of high-throughput gene expression data to identify gene signatures using the genome-wide global significance (GWGS) method. A PPI network was constructed using Cytoscape and clusters that focused on highly connected nodes were obtained using the molecular complex detection (MCODE) clustering algorithm. Pathway analysis was performed to assess the functional relevance of selected gene signatures based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Topological centrality was used to characterize the biological importance of gene signatures, pathways and clusters. The results revealed that, cluster1, as well as the cell cycle and oocyte meiosis pathways were significant subnetworks in the analysis of degree and other centralities, in which hub nodes mostly distributed. The most important hub nodes, with top ranked centrality, were also similar with the common genes from the above three subnetwork intersections, which was viewed as a hub subnetwork with more reproducible than individual critical genes selected without network information. This hub subnetwork attributed to the same biological process which was essential in the function of cell growth and death. This increased the accuracy of identifying gene interactions that took place within the same functional process and was potentially useful for the development of biomarkers and networks for breast cancer.
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View References

1 

Müller A, Homey B, Soto H, et al: Involvement of chemokine receptors in breast cancer metastasis. Nature. 410:50–56. 2001. View Article : Google Scholar : PubMed/NCBI

2 

Chia S, Norris B, Speer C, et al: Human epidermal growth factor receptor 2 overexpression as a prognostic factor in a large tissue microarray series of node-negative breast cancers. J Clin Oncol. 26:5697–5704. 2008. View Article : Google Scholar : PubMed/NCBI

3 

Lisowska KM, Dudaladava V, Jarzab M, et al: BRCA1-related gene signature in breast cancer: the role of ER status and molecular type. Front Biosci (Elite Ed). 3:125–136. 2011. View Article : Google Scholar

4 

Richardson AL, Wang ZC, De Nicolo A, et al: X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell. 9:121–132. 2006. View Article : Google Scholar : PubMed/NCBI

5 

Subramanian A, Tamayo P, Mootha VK, et al: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 102:15545–15550. 2005. View Article : Google Scholar : PubMed/NCBI

6 

Bradley EW, Ruan MM, Vrable A and Oursle MJ: Pathway crosstalk between Ras/Raf and PI3K in promotion of M-CSF-induced MEK/ERK-mediated osteoclast survival. J Cell Biochem. 104:1439–1451. 2008. View Article : Google Scholar : PubMed/NCBI

7 

Gerits N, Kostenko S, Shiryaev A, Johannessen M and Moens U: Relations between the mitogen-activated protein kinase and the cAMP-dependent protein kinase pathways: comradeship and hostility. Cell Signal. 20:1592–1607. 2008. View Article : Google Scholar : PubMed/NCBI

8 

Pham H, Chong B, Vincenti R and Slice LW: Ang II and EGF synergistically induce COX-2 expression via CREB in intestinal epithelial cells. J Cell Physiol. 214:96–109. 2008. View Article : Google Scholar

9 

Wang D, Xia D and Dubois RN: The crosstalk of PTGS2 and EGF signaling pathways in colorectal cancer. Cancers (Basel). 3:3894–3908. 2011. View Article : Google Scholar

10 

Krysan K, Reckamp KL, Dalwadi H, Sharma S, Rozengurt E, Dohadwala M and Dubinett SM: Prostaglandin E2 activates mitogen-activated protein kinase/Erk pathway signaling and cell proliferation in non-small cell lung cancer cells in an epidermal growth factor receptor-independent manner. Cancer Res. 65:6275–6281. 2005. View Article : Google Scholar : PubMed/NCBI

11 

Han JD, Bertin N, Hao T, et al: Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature. 430:88–93. 2004. View Article : Google Scholar : PubMed/NCBI

12 

Ideker T, Ozier O, Schwikowski B and Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 18(Suppl 1): S233–S240. 2002. View Article : Google Scholar : PubMed/NCBI

13 

Chen J and Yuan B: Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics. 22:2283–2290. 2006. View Article : Google Scholar : PubMed/NCBI

14 

Clarke C, Madden SF, Doolan P, 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

15 

Liu W, Peng Y and Tobin DJ: A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis. Peer J. 1:e492013. View Article : Google Scholar : PubMed/NCBI

16 

Diboun I, Wernisch L, Orengo CA and Koltzenburg M: Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics. 7(252): 2006

17 

Wilkinson B: A statistical consideration in psychological research. Psychol Bull. 48:156–158. 1951. 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 

Bader GD and Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 4(2): 2003

20 

Lin WH, Liu WC and Hwang MJ: Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. BMC Syst Biol. 3(32): 2009

21 

Yook SH, Oltvai ZN and Barabási AL: Functional and topological characterization of protein interaction networks. Proteomics. 4:928–942. 2004. View Article : Google Scholar : PubMed/NCBI

22 

Wasserman S and Faust K: Social Network Analysis. Cambridge University Press; Cambridge: 1994, View Article : Google Scholar

23 

Freeman LC: Centered graphs and the construction of ego networks. Math Social Sci. 3:291–304. 1982. View Article : Google Scholar

24 

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

25 

Huang DW, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57. 2008. View Article : Google Scholar

26 

Tranchevent LC, Capdevila FB, Nitsch D, Moor BD, Causmaecker PD and Moreau Y: A guide to web tools to prioritize candidate genes. Brief Bioinform. 12:22–32. 2011. View Article : Google Scholar : PubMed/NCBI

27 

Ozgür A, Vu T, Erkan G and Radev DR: Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics. 24:i277–i285. 2008. View Article : Google Scholar : PubMed/NCBI

28 

Shi L, Jones WD, Jensen RV, et al: The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics. 9(Suppl 9): S102008. View Article : Google Scholar : PubMed/NCBI

29 

Berlingieri MT, Pallante P, Sboner A, et al: UbcH10 is overexpressed in malignant breast carcinomas. Eur J Cancer. 43:2729–2735. 2007. View Article : Google Scholar : PubMed/NCBI

30 

Rutnam ZJ and Yang BB: The non-coding 3′ UTR of CD44 induces metastasis by regulating extracellular matrix functions. J Cell Sci. 125:2075–2085. 2012. View Article : Google Scholar : PubMed/NCBI

31 

Braga-Neto UM and Dougherty ER: Is cross-validation valid for small-sample microarray classification? Bioinformatics. 20:374–380. 2004. View Article : Google Scholar : PubMed/NCBI

32 

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

33 

Palla G, Derényi I, Farkas I and Vicsek T: Uncovering the overlapping community structure of complex networks in nature and society. Nature. 435:814–818. 2005. View Article : Google Scholar : PubMed/NCBI

34 

Estrada E: Virtual identification of essential proteins within the protein interaction network of yeast. Proteomics. 6:35–40. 2006. View Article : Google Scholar

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Copy and paste a formatted citation
Spandidos Publications style
Zhuang D, Jiang L, He Q, Zhou P and Yue T: Identification of hub subnetwork based on topological features of genes in breast cancer. Int J Mol Med 35: 664-674, 2015.
APA
Zhuang, D., Jiang, L., He, Q., Zhou, P., & Yue, T. (2015). Identification of hub subnetwork based on topological features of genes in breast cancer. International Journal of Molecular Medicine, 35, 664-674. https://doi.org/10.3892/ijmm.2014.2057
MLA
Zhuang, D., Jiang, L., He, Q., Zhou, P., Yue, T."Identification of hub subnetwork based on topological features of genes in breast cancer". International Journal of Molecular Medicine 35.3 (2015): 664-674.
Chicago
Zhuang, D., Jiang, L., He, Q., Zhou, P., Yue, T."Identification of hub subnetwork based on topological features of genes in breast cancer". International Journal of Molecular Medicine 35, no. 3 (2015): 664-674. https://doi.org/10.3892/ijmm.2014.2057
Copy and paste a formatted citation
x
Spandidos Publications style
Zhuang D, Jiang L, He Q, Zhou P and Yue T: Identification of hub subnetwork based on topological features of genes in breast cancer. Int J Mol Med 35: 664-674, 2015.
APA
Zhuang, D., Jiang, L., He, Q., Zhou, P., & Yue, T. (2015). Identification of hub subnetwork based on topological features of genes in breast cancer. International Journal of Molecular Medicine, 35, 664-674. https://doi.org/10.3892/ijmm.2014.2057
MLA
Zhuang, D., Jiang, L., He, Q., Zhou, P., Yue, T."Identification of hub subnetwork based on topological features of genes in breast cancer". International Journal of Molecular Medicine 35.3 (2015): 664-674.
Chicago
Zhuang, D., Jiang, L., He, Q., Zhou, P., Yue, T."Identification of hub subnetwork based on topological features of genes in breast cancer". International Journal of Molecular Medicine 35, no. 3 (2015): 664-674. https://doi.org/10.3892/ijmm.2014.2057
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