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Journal of Ovarian Research
Published in: Journal of Ovarian Research 1/2013

Open Access 01-12-2013 | Research

RETRACTED ARTICLE: Investigation of the hub genes and related mechanism in ovarian cancer via bioinformatics analysis

Authors: Ling-jie Fu, Bing Wang

Published in: Journal of Ovarian Research | Issue 1/2013

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Abstract

Background

Ovarian cancer is a cancerous growth arising from the ovary.

Objective

This study was aimed to explore the molecular mechanism of the development and progression of the ovarian cancer.

Methods

We first identified the differentially expressed genes (DEGs) between the ovarian cancer samples and the healthy controls by analyzing the GSE14407 affymetrix microarray data, and then the functional enrichments of the DEGs were investigated. Furthermore, we constructed the protein-protein interaction network of the DEGs using the STRING online tools to find the genes which might play important roles in the progression of ovarian cancer. In addition, we performed the enrichment analysis to the PPI network.

Results

Our study screened 659 DEGs, including 77 up- and 582 down-regulated genes. These DEGs were enriched in pathways such as Cell cycle, p53 signaling pathway, Pathways in cancer and Drug metabolism. CCNE1, CCNB2 and CYP3A5 were the significant genes identified from these pathways. Protein-protein interaction (PPI) network was constructed and network Module A was found closely associated with ovarian cancer. Hub nodes such as VEGFA, CALM1, BIRC5 and POLD1 were found in the PPI network. Module A was related to biological processes such as mitotic cell cycle, cell cycle, nuclear division, and pathways namely Cell cycle, Oocyte meiosis and p53 signaling pathway.

Conclusions

It indicated that ovarian cancer was closely associated to the dysregulation of p53 signaling pathway, drug metabolism, tyrosine metabolism and cell cycle. Besides, we also predicted genes such as CCNE1, CCNB2, CYP3A5 and VEGFA might be target genes for diagnosing the ovarian cancer.
Literature
1.
Jemal A, Siegel R, Ward E, Murray T, Xu J, Thun MJ: Cancer statistics, 2007. CA Cancer J Clin 2007, 57:43–66.CrossRefPubMed
2.
3.
Feeley K, Wells M: Precursor lesions of ovarian epithelial malignancy. Histopathology 2001, 38:87–95.CrossRefPubMed
4.
5.
Goff BA, Mandel L, Muntz HG, Melancon CH: Ovarian carcinoma diagnosis. Cancer 2000, 89:2068–2075.CrossRefPubMed
6.
Lengauer C, Kinzler KW, Vogelstein B: Genetic instabilities in human cancers. Nature 1998, 396:643–649.CrossRefPubMed
7.
Willner J, Wurz K, Allison KH, Galic V, Garcia RL, Goff BA, Swisher EM: Alternate molecular genetic pathways in ovarian carcinomas of common histological types. Hum Pathol 2007, 38:607–613.CrossRefPubMed
8.
Merajver SD, Pham TM, Caduff RF, Chen M, Poy EL, Cooney KA, Weber BL, Collins FS, Johnston C, Frank TS: Somatic mutations in the BRCA1 gene in sporadic ovarian tumours. Nat Genet 1995, 9:439–443.CrossRefPubMed
9.
Nakayama K, Nakayama N, Kurman RJ, Cope L, Pohl G, Samuels Y, Velculescu VE, Wang T-L, Shih I-M: Sequence mutations and amplification of PIK3CA and AKT2 genes in purified ovarian serous neoplasms. Cancer Biol Ther 2006, 5:779–785.CrossRefPubMed
10.
Worsley SD, Ponder BA, Davies BR: Overexpression of cyclin D1 in epithelial ovarian cancers. Gynecol Oncol 1997, 64:189–195.CrossRefPubMed
11.
Sui L, Tokuda M, Ohno M, Hatase O, Hando T: The concurrent expression of p27< sup> kip1</sup> and cyclin D1 in epithelial ovarian tumors. Gynecol Oncol 1999, 73:202–209.CrossRefPubMed
12.
Gilks CB: Subclassification of ovarian surface epithelial tumors based on correlation of histologic and molecular pathologic data. International Journal of Gynecologic Pathology 2004, 23:200–205.CrossRef
13.
Bowen NJ, Walker LD, Matyunina LV, Logani S, Totten KA, Benigno BB, McDonald JF: Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells. BMC Med Genomics 2009, 2:71.CrossRefPubMedPubMedCentral
14.
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249–264.CrossRefPubMed
15.
Team R: R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria, 2007. Book R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2007 2012. ISBN 3–900051–07–0
16.
Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK: A comparison of background correction methods for two-colour microarrays. Bioinformatics 2007, 23:2700–2707.CrossRefPubMed
17.
18.
Alvord G, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA: The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 2007, 8:R183.CrossRefPubMedPubMedCentral
19.
Srihari S, Leong HW: Temporal dynamics of protein complexes in PPI networks: a case study using yeast cell cycle dynamics. BMC bioinformatics 2012,13(Suppl 17):S16.PubMedPubMedCentral
20.
von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B: STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 2003, 31:258–261.CrossRefPubMedPubMedCentral
21.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498–2504.CrossRefPubMedPubMedCentral
22.
23.
Maraziotis IA, Dimitrakopoulou K, Bezerianos A: An in silico method for detecting overlapping functional modules from composite biological networks. BMC Syst Biol 2008, 2:93.CrossRefPubMedPubMedCentral
24.
DeRycke MS, Pambuccian SE, Gilks CB, Kalloger SE, Ghidouche A, Lopez M, Bliss RL, Geller MA, Argenta PA, Harrington KM: Nectin 4 overexpression in ovarian cancer tissues and serum potential role as a serum biomarker. Am J Clin Pathol 2010, 134:835–845.CrossRefPubMedPubMedCentral
25.
Balch C, Huang TH, Brown R, Nephew KP: The epigenetics of ovarian cancer drug resistance and resensitization. Am J Obstet Gynecol 2004, 191:1552–1572.CrossRefPubMed
26.
Reles A, Wen WH, Schmider A, Gee C, Runnebaum IB, Kilian U, Jones LA, El-Naggar A, Minguillon C, Schönborn I: Correlation of p53 mutations with resistance to platinum-based chemotherapy and shortened survival in ovarian cancer. Clin Cancer Res 2001, 7:2984–2997.PubMed
27.
Jabbour AM, Gordon L, Daunt CP, Green BD, Kok CH, D'Andrea R, Ekert PG: p53-Dependent transcriptional responses to interleukin-3 signaling. PloS One 2012, 7:e31428.CrossRefPubMedPubMedCentral
28.
Nakayama N, Nakayama K, Shamima Y, Ishikawa M, Katagiri A, Iida K, Miyazaki K: Gene amplification CCNE1 is related to poor survival and potential therapeutic target in ovarian cancer. Cancer 2010, 116:2621–2634.CrossRefPubMed
29.
SLAV D, Bar I, Sandbank J: Usefulness of CDK5RAP3, CCNB2, and RAGE genes for the diagnosis of lung adenocarcinoma. Int J Biol Markers 2007, 22:108–113.
30.
Rodriguez-Antona C, Ingelman-Sundberg M: Cytochrome P450 pharmacogenetics and cancer. Oncogene 2006, 25:1679–1691.CrossRefPubMed
31.
Jia J, Li B, Jin Y, Wang D: Expression, purification, and characterization of human tyrosyl-tRNA synthetase. Protein Expr Purif 2003, 27:104–108.CrossRefPubMed
32.
Morotti M, Becker CM, Menada MV, Ferrero S: Targeting tyrosine-kinases in ovarian cancer. Expert Opin Investig Drugs 2013,22(10):1265–79.CrossRefPubMed
33.
Bains RK, Kovacevic M, Plaster CA, Tarekegn A, Bekele E, Bradman NN, Thomas MG: Molecular diversity and population structure at the cytochrome P450 3A5 gene in Africa. BMC genetics 2013, 14:34.CrossRefPubMedPubMedCentral
34.
Downie D, McFadyen MC, Rooney PH, Cruickshank ME, Parkin DE, Miller ID, Telfer C, Melvin WT, Murray GI: Profiling cytochrome P450 expression in ovarian cancer: identification of prognostic markers. Clin Cancer Res 2005, 11:7369–7375.CrossRefPubMed
35.
Ferrara N, Gerber H-P, LeCouter J: The biology of VEGF and its receptors. Nat Med 2003, 9:669–676.CrossRefPubMed
36.
Awata T, Inoue K, Kurihara S, Ohkubo T, Watanabe M, Inukai K, Inoue I, Katayama S: A common polymorphism in the 5′-untranslated region of the VEGF gene is associated with diabetic retinopathy in type 2 diabetes. Diabetes 2002, 51:1635–1639.CrossRefPubMed
37.
Herr D, Sallmann A, Bekes I, Konrad R, Holzheu I, Kreienberg R, Wulff C: VEGF induces ascites in ovarian cancer patients via increasing peritoneal permeability by downregulation of Claudin 5. Gynecol Oncol 2012, 127:210–216.CrossRefPubMed
Metadata
Title
RETRACTED ARTICLE: Investigation of the hub genes and related mechanism in ovarian cancer via bioinformatics analysis
Authors
Ling-jie Fu
Bing Wang
Publication date
01-12-2013
Publisher
BioMed Central
Published in
Journal of Ovarian Research / Issue 1/2013
Electronic ISSN: 1757-2215
DOI
https://doi.org/10.1186/1757-2215-6-92

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