title: Identification of therapeutic targets for breast cancer using biological informatics methods.
abstract: The present study aimed to investigate the modular mechanisms underlying breast cancer and identify potential targets for breast cancer treatment. The differentially expressed genes (DEGs) between breast cancer and normal cells were assessed using microarray data obtained from the Gene Expression Omnibus database. Gene ontology (GO) and pathway enrichment analyses were performed in order to investigate the functions of these DEGs. Subsequently, the protein-protein interaction (PPI) network was constructed using the Cytoscape software. The identified subnetworks were further analyzed using the Molecular Complex Detection plugin. In total, 571 genes (241 upregulated and 330 downregulated genes) were found to be differentially expressed between breast cancer and normal cells. The GO terms significantly enriched by DEGs included cell adhesion, immune response and extracellular region, while the most significant pathways included focal adhesion and complement and coagulation cascade pathways. The PPI network was established with 273 nodes and 718 edges, while fibronectin 1 (FN1, degrees score, 39), interleukin 6 (IL6; degree score, 96) and c-Fos protein (degree score, 32) were identified as the hub proteins in subnetwork 2. These dysregulated genes were found to be involved in the development of breast cancer. The FN1, IL6 and FOS genes may therefore be potential targets in the treatment of breast cancer.
authors.affiliation: Department of Oncology, The People's Hospital of Linyi Economic and Technological Development Zone, Linyi, Shandong 276023, P.R. China.
authors.forename: Xuejian
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Histological Embryology, Shandong Medical College, Linyi, Shandong 276000, P.R. China.
authors.forename: Yongzhen
authors.initials: Y
authors.lastname: Ma
authors.affiliation: Department of Oncology, The People's Hospital of Linyi Economic and Technological Development Zone, Linyi, Shandong 276023, P.R. China.
authors.forename: Wenchuan
authors.initials: W
authors.lastname: Yang
authors.affiliation: Department of Oncology, The People's Hospital of Linyi Economic and Technological Development Zone, Linyi, Shandong 276023, P.R. China.
authors.forename: Xia
authors.initials: X
authors.lastname: Wu
authors.affiliation: Department of Oncology, The People's Hospital of Linyi Economic and Technological Development Zone, Linyi, Shandong 276023, P.R. China.
authors.forename: Lihua
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Department of Oncology, The People's Hospital of Linyi Economic and Technological Development Zone, Linyi, Shandong 276023, P.R. China.
authors.forename: Xiangli
authors.initials: X
authors.lastname: Chen
mesh_terms: D001943:Breast Neoplasms / Q000378:metabolism / Q000473:pathology* / Q000628:therapy; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D005260:Female; D005353:Fibronectins / Q000235:genetics / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D015850:Interleukin-6 / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D060066:Protein Interaction Maps; D016760:Proto-Oncogene Proteins c-fos / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: C067625:FN1 protein, human; D005353:Fibronectins; D015850:Interleukin-6; D016760:Proto-Oncogene Proteins c-fos
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Rev Environ Health. 2008 Jan-Mar;23(1):1-37
references.pmid: 18557596
references.citation: Eur J Cancer. 2005 Nov;41(16):2449-61
references.pmid: 16199154
references.citation: Biomed Pharmacother. 2012 Apr;66(3):228-31
references.pmid: 22425183
references.citation: Cancer Res. 2013 Jun 1;73(11):3470-80
references.pmid: 23633491
references.citation: FASEB J. 1990 Aug;4(11):2868-80
references.pmid: 2199285
references.citation: J Natl Cancer Inst. 2004 Jun 16;96(12):926-35
references.pmid: 15199112
references.citation: Radiology. 1991 Jul;180(1):177-84
references.pmid: 2052688
references.citation: J Clin Invest. 1998 Jan 15;101(2):311-20
references.pmid: 9435302
references.citation: Dis Markers. 2005;21(3):157-65
references.pmid: 16276011
references.citation: J Mammary Gland Biol Neoplasia. 1998 Jan;3(1):63-72
references.pmid: 10819505
references.citation: Br J Surg. 2013 Jan;100(2):252-60
references.pmid: 23175431
references.citation: PLoS One. 2011;6(5):e18640
references.pmid: 21611158
references.citation: Cancer Res. 2004 Sep 1;64(17):6071-4
references.pmid: 15342389
references.citation: J Cell Sci. 2002 Oct 15;115(Pt 20):3861-3
references.pmid: 12244123
references.citation: Cancer Res. 1999 Nov 1;59(21):5475-8
references.pmid: 10554021
references.citation: Cancer Lett. 1995 Nov 6;97(2):225-31
references.pmid: 7497467
references.citation: Nature. 2002 Jan 31;415(6871):530-6
references.pmid: 11823860
references.citation: Biostatistics. 2003 Apr;4(2):249-64
references.pmid: 12925520
references.citation: Nature. 1990 Aug 2;346(6283):425-34
references.pmid: 1974032
references.citation: Am J Clin Pathol. 1996 Apr;105(4):394-402
references.pmid: 8604681
references.citation: Mol Cell Biol. 1991 Oct;11(10):5032-43
references.pmid: 1922031
references.citation: Oncologist. 2002;7(1):60-4
references.pmid: 11854547
references.citation: Lab Invest. 1993 Jan;68(1):4-17
references.pmid: 8423675
references.citation: Lancet. 2005 Feb 19-25;365(9460):671-9
references.pmid: 15721472
references.citation: Chem Biol Interact. 2014 Mar 5;210:51-63
references.pmid: 24365254
references.citation: Cell. 1996 Feb 9;84(3):345-57
references.pmid: 8608588
references.citation: Clin Cancer Res. 2001 Dec;7(12 Suppl):4429s-4435s; discussion 4411s-4412s
references.pmid: 11916236
references.citation: Cancer Epidemiol Biomarkers Prev. 2003 Sep;12(9):920-5
references.pmid: 14504205
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8
references.pmid: 21045058
references.citation: Cell. 2013 Oct 10;155(2):384-96
references.pmid: 24120137
references.citation: Cancer Res. 2008 Jul 1;68(13):5004-8
references.pmid: 18593897
references.citation: Endocrinology. 2009 Jan;150(1):14-23
references.pmid: 18787018
references.citation: Eur J Endocrinol. 2004 Mar;150(3):243-55
references.pmid: 15012607
references.citation: N Engl J Med. 2006 Jan 19;354(3):270-82
references.pmid: 16421368
references.citation: Oncogene. 1995 Jun 15;10(12):2435-46
references.pmid: 7784095
references.citation: Cancer Res. 2011 Nov 1;71(21):6857-66
references.pmid: 21908556
references.citation: Oncol Lett. 2012 Apr 1;3(4):787-790
references.pmid: 22740994
references.citation: BMC Bioinformatics. 2003 Jan 13;4:2
references.pmid: 12525261
references.citation: Methods Mol Biol. 2011;696:291-303
references.pmid: 21063955
references.citation: BMC Genomics. 2005 May 03;6:60
references.pmid: 15869710
references.citation: Stat Appl Genet Mol Biol. 2004;3:Article3
references.pmid: 16646809
references.citation: Nat Med. 2001 May;7(5):552-6
references.pmid: 11329055
references.citation: Cancer Res. 1993 Apr 1;53(7):1696-701
references.pmid: 8453644