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

Open Access 01-12-2013 | Research

RETRACTED ARTICLE: Gene-gene interaction network analysis of ovarian cancer using TCGA data

Authors: Huanchun Ying, Jing Lv, Tianshu Ying, Shanshan Jin, Jingru Shao, Lili Wang, Hongying Xu, Bin Yuan, Qing Yang

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

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Abstract

Background

The Cancer Genome Atlas (TCGA) Data portal provides a platform for researchers to search, download, and analysis data generated by TCGA. The objective of this study was to explore the molecular mechanism of ovarian cancer pathogenesis.

Methods

Microarray data of ovarian cancer were downloaded from TCGA database, and Limma package in R language was used to identify the differentially expressed genes (DEGs) between ovarian cancer and normal samples, followed by the function and pathway annotations of the DEGs. Next, NetBox software was used to for the gene-gene interaction (GGI) network construction and the corresponding modules identification, and functions of genes in the modules were screened using DAVID.

Results

Our studies identified 332 DEGs, including 146 up-regulated genes which mainly involved in the cell cycle related functions and cell cycle pathway, and 186 down-regulated genes which were enriched in extracellular region par function, and Ether lipid metabolism pathway. GGI network was constructed by 127 DEGs and their significantly interacted 209 genes (LINKERs). In the top 10 nodes ranked by degrees in the network, 5 were LINKERs. Totally, 7 functional modules in the network were selected, and they were enriched in different functions and pathways, such as mitosis process, DNA replication and DNA double-strand synthesis, lipid synthesis processes and metabolic pathways. AR, BRCA1, TFDP1, FOXM1, CDK2, and DBF4 were identified as the transcript factors of the 7 modules.

Conclusion

our data provides a comprehensive bioinformatics analysis of genes, functions, and pathways which may be involved in the pathogenesis of ovarian cancer.
Literature
1.
Braun R, Finney R, Yan C, Chen Q-R, Hu Y, Edmonson M, Meerzaman D, Buetow K: Discovery analysis of TCGA data reveals association between germline genotype and survival in ovarian cancer patients. PLoS One 2013, 8:e55037.CrossRefPubMedPubMedCentral
2.
Grzankowski KS, Carney M: Quality of life in ovarian cancer. Cancer Control 2011, 18:52–58.PubMed
3.
Bell D, Berchuck A, Birrer M, Chien J, Cramer D, Dao F, Dhir R, DiSaia P, Gabra H, Glenn P: Integrated genomic analyses of ovarian carcinoma. 2011.
4.
Bolton KL, Ganda C, Berchuck A, Pharaoh PD, Gayther SA: Role of common genetic variants in ovarian cancer susceptibility and outcome: progress to date from the ovarian cancer association consortium (OCAC). J Int Med 2012, 271:366–378.CrossRef
5.
Liang D, Meyer L, Chang DW, Lin J, Pu X, Ye Y, Gu J, Wu X, Lu K: Genetic variants in MicroRNA biosynthesis pathways and binding sites modify ovarian cancer risk, survival, and treatment response. Cancer Res 2010, 70:9765–9776.CrossRefPubMed
6.
Cancer Genome Atlas Research Network: Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474:609–615.CrossRef
7.
Ratner E, Lu L, Boeke M, Barnett R, Nallur S, Chin LJ, Pelletier C, Blitzblau R, Tassi R, Paranjape T: A KRAS-variant in ovarian cancer acts as a genetic marker of cancer risk. Cancer Res 2010, 70:6509–6515.CrossRefPubMedPubMedCentral
8.
Ying H, Lv J, Ying T, Li J, Yang Q: Screening of feature genes of the ovarian cancer epithelia with DNA microarray. J Ovar Res 2013, 6:1–8.CrossRef
9.
Chang H, Fontenay GV, Han J, Cong G, Baehner FL, Gray JW, Spellman PT, Parvin B: Morphometic analysis of TCGA glioblastoma multiforme. BMC Bioinformatics 2011, 12:484.CrossRefPubMedPubMedCentral
10.
Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S: Bioinformatics and computational biology solutions using R and bioconductor: vol. 746718470. Statistics for Biology and Health: Springer New York; 2005.CrossRef
11.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology: tool for the unification of biology. Nat Genet 2000, 25:25–29.CrossRefPubMedPubMedCentral
12.
Kanehisa M: The KEGG database. 2002. [Novartis found symp]
13.
Prasad TK, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A: Human protein reference database—2009 update. Nucleic Acids Res 2009, 37:D767-D772.CrossRef
14.
Joshi-Tope G, Gillespie M, Vastrik I, D’Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath G, Wu G, Matthews L: Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, 33:D428-D432.CrossRefPubMedPubMedCentral
15.
16.
Somwar R, Erdjument-Bromage H, Larsson E, Shum D, Lockwood WW, Yang G, Sander C, Ouerfelli O, Tempst PJ, Djaballah H: Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell lines. Proc Natl Acad Sci 2011, 108:16375–16380.CrossRefPubMedPubMedCentral
17.
Wan S-M, Lv F, Guan T: Identification of genes and microRNAs involved in ovarian carcinogenesis. Asian Pac J Cancer Prev 2012, 13:3997–4000.CrossRefPubMed
18.
Kimura N, Takizawa M, Okita K, Natori O, Igarashi K, Ueno M, Nakashima K, Nobuhisa I, Taga T: Identification of a novel transcription factor, ELYS, expressed predominantly in mouse foetal haematopoietic tissues. Genes Cells 2002, 7:435–446.CrossRefPubMed
19.
Turashvili G, Bouchal J, Baumforth K, Wei W, Dziechciarkova M, Ehrmann J, Klein J, Fridman E, Skarda J, Srovnal J: Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis. BMC Cancer 2007, 7:55.CrossRefPubMedPubMedCentral
20.
Perales G, Burguete-García AI, Dimas J, Bahena-Román M, Bermúdez-Morales VH, Moreno J, Madrid-Marina V: A polymorphism in the AT-hook motif of the transcriptional regulator AKNA is a risk factor for cervical cancer. Biomarkers 2010, 15:470–474.CrossRefPubMed
21.
Chea E: Regulation of planar cell polarity and Vangl2 trafficking by Tmem14a. 2012.
22.
Ghafouri-Fard S, Modarressi M-H: Expression of cancer–testis genes in brain tumors: implications for cancer immunotherapy. Future Oncol 2012, 8:961–987.CrossRef
23.
24.
Pacurari M, Qian Y, Porter D, Wolfarth M, Wan Y, Luo D, Ding M, Castranova V, Guo N: Multi-walled carbon nanotube-induced gene expression in the mouse lung: association with lung pathology. Toxicol Appl Pharmacol 2011, 255:18–31.CrossRefPubMedPubMedCentral
25.
Tatarano S, Chiyomaru T, Kawakami K, Enokida H, Yoshino H, Hidaka H, Yamasaki T, Kawahara K, Nishiyama K, Seki N: miR-218 on the genomic loss region of chromosome 4p15. 31 functions as a tumor suppressor in bladder cancer. Inter J Oncol 2011, 39:13–21.
26.
Gayther SA, Song H, Ramus SJ, Kjaer SK, Whittemore AS, Quaye L, Tyrer J, Shadforth D, Hogdall E, Hogdall C: Tagging single nucleotide polymorphisms in cell cycle control genes and susceptibility to invasive epithelial ovarian cancer. Cancer Res 2007, 67:3027–3035.CrossRefPubMed
27.
28.
Laoukili J, Stahl M, Medema RH: FoxM1: at the crossroads of ageing and cancer: biochimica et biophysica acta (BBA)-reviews on. Cancer 2007, 1775:92–102.
29.
Marone M, Scambia G, Giannitelli C, Ferrandina G, Masciullo V, Bellacosa A, Benedetti‒Panici P, Mancuso S: Analysis of cyclin E and CDK2 in ovarian cancer: gene amplification and RNA overexpression. Intern J Cancer 1998, 75:34–39.CrossRef
30.
31.
Montagnoli A, Moll J, Colotta F: Targeting cell division cycle 7 kinase: a new approach for cancer therapy. Clin Cancer Res 2010, 16:4503–4508.CrossRefPubMed
32.
Elattar A, Warburton KG, Mukhopadhyay A, Freer RM, Shaheen F, Cross P, Plummer ER, Robson CN, Edmondson RJ: Androgen receptor expression is a biological marker for androgen sensitivity in high grade serous epithelial ovarian cancer. Gynecol Oncol 2012, 124:142–147.CrossRefPubMed
33.
Audeh MW, Carmichael J, Penson RT, Friedlander M, Powell B, Bell-McGuinn KM, Scott C, Weitzel JN, Oaknin A, Loman N: Oral poly (ADP-ribose) polymerase inhibitor olaparib in patients with< i> BRCA1</i> or< i> BRCA2</i> mutations and recurrent ovarian cancer: a proof-of-concept trial. Lancet 2010, 376:245–251.CrossRefPubMed
34.
Zhang S, Royer R, Li S, McLaughlin JR, Rosen B, Risch HA, Fan I, Bradley L, Shaw PA, Narod SA: Frequencies of BRCA1 and BRCA2 mutations among 1,342 unselected patients with invasive ovarian cancer. Gynecol Oncol 2011, 121:353–357.CrossRefPubMed
35.
Shin SM, Chung YJ, Oh ST, Jeon HM, Hwang LJ, Namkoong H, Kim HK, Cho GW, Hur SY, Kim TE: HCCR-1–interacting molecule “deleted in polyposis 1” plays a tumor-suppressor role in colon carcinogenesis. Gastroenterology 2006, 130:2074–2086.CrossRefPubMed
Metadata
Title
RETRACTED ARTICLE: Gene-gene interaction network analysis of ovarian cancer using TCGA data
Authors
Huanchun Ying
Jing Lv
Tianshu Ying
Shanshan Jin
Jingru Shao
Lili Wang
Hongying Xu
Bin Yuan
Qing Yang
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/10.1186/1757-2215-6-88

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