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Article

Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes

  • Authors:
    • Yong Sun
    • Kai Yuan
    • Peng Zhang
    • Rong Ma
    • Qi‑Wen Zhang
    • Xing‑Song Tian
  • View Affiliations / Copyright

    Affiliations: Department of Breast and Thyroid Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, P.R. China, Department of Breast Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, P.R. China, Department of General Surgery, Laiwu Hospital Affiliated to Taishan Medical College, Laiwu, Shandong 271100, P.R. China, Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
  • Pages: 743-748
    |
    Published online on: May 27, 2015
       https://doi.org/10.3892/etm.2015.2527
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Abstract

Multiple signal transduction pathways can affect each other considerably through crosstalk. However, the presence and extent of this phenomenon have not been rigorously studied. The aim of the present study was to identify strong and normal interactions between pathways in breast cancer and determine the main pathway. Five sets of breast cancer data were downloaded from the high‑throughput Gene Expression Omnibus (GEO) and analyzed to identify differentially expressed (DE) genes using the Rank Product (RankProd) method. A list of pathways with differential expression was obtained by gene set enrichment analysis (GSEA) of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The DE genes that overlapped between pathways were identified and a crosstalk network diagram based on the overlap of DE genes was constructed. A total of 1,464 DE genes and 26 pathways were identified. In addition, the number of DE genes that overlapped between specific pathways were determined, and the greatest degree of overlap was between the extracellular matrix (ECM)‑receptor interaction and Focal adhesion pathways, which had 22 overlapping DE genes. Weighted pathway analysis of the crosstalk between pathways identified that Pathways in cancer was the main pathway in breast cancer.
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1 

Igene H: Global health inequalities and breast cancer: An impending public health problem for developing countries. Breast J. 14:428–434. 2008. View Article : Google Scholar : PubMed/NCBI

2 

Chia S, Norris B, Speers 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 

Planas-Silva MD, Bruggeman RD, Grenko RT and Smith JS: Overexpression of c-Myc and Bcl-2 during progression and distant metastasis of hormone-treated breast cancer. Exp Mol Pathol. 82:85–90. 2007. View Article : Google Scholar : PubMed/NCBI

4 

Ota D, Mimori K, Yokobori T, et al: Identification of recurrence-related microRNAs in the bone marrow of breast cancer patients. Int J Oncol. 38:955–962. 2011.PubMed/NCBI

5 

Ohira M and Nakagawara A: Global genomic and RNA profiles for novel risk stratification of neuroblastoma. Cancer Sci. 101:2295–2301. 2010. View Article : Google Scholar : PubMed/NCBI

6 

Fujita T, Ikeda H, Kawasaki K, Taira N, Ogasawara Y, Nakagawara A and Doihara H: Clinicopathological relevance of UbcH10 in breast cancer. Cancer Sci. 100:238–248. 2009. View Article : Google Scholar : PubMed/NCBI

7 

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

8 

Wang S, Chen C, Meng Y, et al: Effective suppression of breast tumor growth by an anti-EGFR/ErbB2 bispecific antibody. Cancer Lett. 325:214–219. 2012. View Article : Google Scholar : PubMed/NCBI

9 

Tinnikov AA, Yeung KT, Das S and Samuels HH: Identification of a novel pathway that selectively modulates apoptosis of breast cancer cells. Cancer Res. 69:1375–1382. 2009. View Article : Google Scholar : PubMed/NCBI

10 

Donato M, Xu Z, Tomoiaga A, et al: Analysis and correction of crosstalk effects in pathway analysis. Genome Res. 23:1885–1893. 2013. View Article : Google Scholar : PubMed/NCBI

11 

Bradley EW, Ruan MM, Vrable A and Oursler 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

12 

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

13 

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 : PubMed/NCBI

14 

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 : PubMed/NCBI

15 

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

16 

Wang C, Cigliano A, Delogu S, Armbruster J, et al: Functional crosstalk between AKT/mTOR and Ras/MAPK pathways in hepatocarcinogenesis: Implications for the treatment of human liver cancer. Cell Cycle. 12:1999–2010. 2013. View Article : Google Scholar : PubMed/NCBI

17 

Hong FX, Breitling R, McEntee CW, Wittner BS, Nemhauser JL and Chory J: A bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics. 22:2825–2827. 2006. View Article : Google Scholar : PubMed/NCBI

18 

Mootha VK, Lindgren CM, Eriksson KF, et al: PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 34:267–273. 2003. View Article : Google Scholar : PubMed/NCBI

19 

Suárez-Fariñas M, Lowes MA, Zaba LC and Krueger JG: Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA). PLoS ONE. 5:e102472010. View Article : Google Scholar : PubMed/NCBI

20 

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

21 

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 : PubMed/NCBI

22 

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

23 

Efron B and Tibshirani R: Empirical Bayes methods and false discovery rates for microarrays. Genet Epidemiol. 23:70–86. 2002. View Article : Google Scholar : PubMed/NCBI

24 

Cui X and Churchill GA: Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 4:2102003. View Article : Google Scholar : PubMed/NCBI

25 

Yekutieli D and Benjamini Y: Resampling-based false discovery rate controlling multiple test procedures for correlated test statistics. J Stat Plan Inference. 82:171–196. 1999. View Article : Google Scholar

26 

Breitling R and Herzyk P: Rank-based methods as a non-parametric alternative of the T-statistic for the analysis of biological microarray data. J Bioinform Comput Biol. 3:1171–1189. 2005. View Article : Google Scholar : PubMed/NCBI

27 

Long JM, Bell CW, Fagg WS IV, et al: Microarray and pathway analysis reveals decreased CDC25A and increased CDC42 associated with slow growth of BCL2 overexpressing immortalized breast cell line. Cell Cycle. 7:3062–3073. 2008. View Article : Google Scholar : PubMed/NCBI

28 

Bissell MJ, Radisky DC, Rizki A, Weaver VM and Petersen OW: The organizing principle: Microenvironmental influences in the normal and malignant breast. Differentiation. 70:537–546. 2002. View Article : Google Scholar : PubMed/NCBI

29 

Huan J, Wang L, Xing L, et al: Insights into significant pathways and gene interaction networks underlying breast cancer cell line MCF-7 treated with 17β-estradiol (E2). Gene. 533:346–355. 2014. View Article : Google Scholar : PubMed/NCBI

30 

del Sol A, Balling R, Hood L and Galas D: Diseases as network perturbations. Curr Opin Biotechnol. 21:566–571. 2010. View Article : Google Scholar : PubMed/NCBI

31 

Miller JA, Oldham MC and Geschwind DH: A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci. 28:1410–1420. 2008. View Article : Google Scholar : PubMed/NCBI

32 

Shao L, Wang L, Wei Z, et al: Dynamic network of transcription and pathway crosstalk to reveal molecular mechanism of MGd-treated human lung cancer cells. PLoS ONE. 7:e319842012. View Article : Google Scholar : PubMed/NCBI

33 

Tian M, Chen X, Xiong Q, et al: Phosphoproteomic analysis of protein phosphorylation networks in Tetrahymena thermophila, a model single-celled organism. Mol Cell Proteomics. 13:503–519. 2014. View Article : Google Scholar : PubMed/NCBI

34 

Bartlett TE, Olhede SC and Zaikin A: A DNA methylation network interaction measure, and detection of network oncomarkers. PLoS ONE. 9:e845732014. View Article : Google Scholar : PubMed/NCBI

35 

Remon J, Morán T, Reguart N, Majem M, Carcereny E and Lianes P: Beyond EGFR TKI in EGFR-mutant non-small cell lung cancer patients: Main challenges still to be overcome. Cancer Treat Rev. 40:723–729. 2014. View Article : Google Scholar : PubMed/NCBI

36 

Wang Z, Wang Z, Liang Z, et al: Expression and clinical significance of IGF-1, IGFBP-3, and IGFBP-7 in serum and lung cancer tissues from patients with non-small cell lung cancer. Onco Targets Ther. 6:1437–1444. 2013.PubMed/NCBI

37 

Bilke S, Schwentner R, Yang F, et al: Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer. Genome Res. 23:1797–1809. 2013. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Sun Y, Yuan K, Zhang P, Ma R, Zhang QW and Tian XS: Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes. Exp Ther Med 10: 743-748, 2015.
APA
Sun, Y., Yuan, K., Zhang, P., Ma, R., Zhang, Q., & Tian, X. (2015). Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes. Experimental and Therapeutic Medicine, 10, 743-748. https://doi.org/10.3892/etm.2015.2527
MLA
Sun, Y., Yuan, K., Zhang, P., Ma, R., Zhang, Q., Tian, X."Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes". Experimental and Therapeutic Medicine 10.2 (2015): 743-748.
Chicago
Sun, Y., Yuan, K., Zhang, P., Ma, R., Zhang, Q., Tian, X."Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes". Experimental and Therapeutic Medicine 10, no. 2 (2015): 743-748. https://doi.org/10.3892/etm.2015.2527
Copy and paste a formatted citation
x
Spandidos Publications style
Sun Y, Yuan K, Zhang P, Ma R, Zhang QW and Tian XS: Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes. Exp Ther Med 10: 743-748, 2015.
APA
Sun, Y., Yuan, K., Zhang, P., Ma, R., Zhang, Q., & Tian, X. (2015). Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes. Experimental and Therapeutic Medicine, 10, 743-748. https://doi.org/10.3892/etm.2015.2527
MLA
Sun, Y., Yuan, K., Zhang, P., Ma, R., Zhang, Q., Tian, X."Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes". Experimental and Therapeutic Medicine 10.2 (2015): 743-748.
Chicago
Sun, Y., Yuan, K., Zhang, P., Ma, R., Zhang, Q., Tian, X."Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes". Experimental and Therapeutic Medicine 10, no. 2 (2015): 743-748. https://doi.org/10.3892/etm.2015.2527
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