Differential co-expression analysis of a microarray gene expression profiles of pulmonary adenocarcinoma

Molecular Medicine Reports

Volumn 10, Issue 2, 2014, Pages 713-718

  Fu, Shijie ^a   Pan, Xufeng ^a   Fang, Wentao ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

Differentially co expressed genes; Pathway; Pulmonary adenocarcinoma

Indexed keywords

ADENOSINE TRIPHOSPHATASE (CALCIUM); CYCLIN DEPENDENT KINASE INHIBITOR 1A; HYPOXIA INDUCIBLE FACTOR 1ALPHA; LYMPHOID ENHANCER FACTOR 1; NUCLEAR RECEPTOR NUR77; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; TRANSCRIPTION FACTOR ETS; TRANSCRIPTION FACTOR FLI 1; TRANSCRIPTION FACTOR JUND; UROKINASE; VIMENTIN; VITAMIN D RECEPTOR; TRANSCRIPTOME;

ARTICLE; BIOINFORMATICS; CANCER TISSUE; COMPARATIVE STUDY; CONTROLLED STUDY; DIFFERENTIALLY COEXPRESSED GENE; DNA REPLICATION; GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GLUCONEOGENESIS; GLYCOLYSIS; HUMAN; HUMAN TISSUE; LUNG ADENOCARCINOMA; MICROARRAY ANALYSIS; PROTO ONCOGENE; REGULATORY MECHANISM; TRANSCRIPTION REGULATION; ADENOCARCINOMA; DNA MICROARRAY; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; LUNG TUMOR; METABOLISM; PATHOLOGY;

ADENOCARCINOMA; DATABASES, GENETIC; GENE REGULATORY NETWORKS; HUMANS; LUNG NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTOME;

EID: 84903315688     PISSN: 17912997     EISSN: 17913004     Source Type: Journal    
DOI: 10.3892/mmr.2014.2300     Document Type: Article

References (49)

1. Ferlay J, Shin HR, Bray F, Forman D, Mathers C and Parkin DM: Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer 127: 2893-2917, 2010.
2. Jemal A, Center MM, DeSantis C and Ward EM: Global patterns of cancer incidence and mortality rates and trends. Cancer Epidemiol Biomarkers Prev 19: 1893-1907, 2010.
3. Mackay J, Eriksen M and Shafey O (eds): The Tobacco Atlas. 2nd edition, American Cancer Society, Atlanta, GA, 2006.
4. Hong WK, Bast RC, Hait WN, Kufe DW, Pollock RE, Weichselbaum RR, Holland HF and Frei E III (eds): Cancer Medicine. 8th edition, PMPH, New York, NY, 2010.
5. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, et al: Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA 98: 13784-13789, 2001. (Pubitemid 33115976)
6. Director's Challenge Consortium for the Molecular Classification of Lung Adenocarcinoma; Shedden K, Taylor JM, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, Eschrich S, Jurisica I, Giordano TJ, Misek DE, et al: Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008; 14: 822-827.
7. Stearman RS, Dwyer-Nield L, Zerbe L, Blaine SA, Chan Z, Bunn PA Jr, Johnson GL, Hirsch FR, Merrick DT, Franklin WA, et al: Analysis of orthologous gene expression between human pulmonary adenocarcinoma and a carcinogen-induced murine model. Am J Pathol 167: 1763-1775, 2005. (Pubitemid 41713326)
8. Jiang H, Deng Y, Chen HS, Tao L, Sha Q, Chen J, Tsai CJ and Zhang S: Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinformatics 5: 81, 2004.
9. Ron D, Chen CH, Caldwell J, Jamieson L, Orr E and Mochly-Rosen D: Cloning of an intracellular receptor for protein kinase C: a homolog of the beta subunit of G proteins. Proc Natl Acad Sci USA 91: 839-843, 1994. (Pubitemid 24048462)
10. Nagashio R, Sato Y, Matsumoto T, Kageyama T, Satoh Y, Shinichiro R, Masuda N, Goshima N, Jiang SX and Okayasu I: Expression of RACK1 is a novel biomarker in pulmonary adenocarcinomas. Lung Cancer 69: 54-59, 2010.
11. Saito RA, Watabe T, Horiguchi K, Kohyama T, Saitoh M, Nagase T and Miyazono K: Thyroid transcription factor-1 inhibits transforming growth factor-β-mediated epithelial-to-mesenchymal transition in lung adenocarcinoma cells. Cancer Res 69: 2783-2791, 2009.
12. Fang G, Kuang R, Pandey G, Steinbach M, Myers CL and Kumar V: Subspace differential coexpression analysis: problem definition and a general approach. Pac Symp Biocomput: 145-156, 2010.
13. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U and Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264, 2003.
14. 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.
15. Lee HK, Hsu AK, Sajdak J, Qin J and Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res 14: 1085-1094, 2004. (Pubitemid 38811545)
16. Stuart JM, Segal E, Koller D and Kim SK: A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255, 2003. (Pubitemid 37248749)
17. Liu BH, Yu H, Tu K, Li C, Li YX and Li YY: DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data. Bioinformatics 26: 2637-2638, 2010.
18. Yu H, Liu BH, Ye ZQ, Li C, Li YX and Li YY: Link-based quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics 12: 315, 2011.
19. Kanehisa M and Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30, 2000. (Pubitemid 30047706)
20. Huang da W, Sherman BT, Tan Q, Collins JR, Alvord G, Roayaei J, Stephens R, Baseler MW, Lane HC and Lempicki RA. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 8: R183, 2007.
21. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Prüss M, Reuter I and Schacherer F: TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28: 316-319, 2000. (Pubitemid 30047792)
22. Smoot ME, Ono K, Ruscheinski J, Wang PL and Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432, 2011.
23. Chen G, Gharib TG, Wang H, Huang CC, Kuick R, Thomas DG, Shedden KA, Misek DE, Taylor JM, Giordano TJ, et al: Protein profiles associated with survival in lung adenocarcinoma. Proc Natl Acad Sci USA 100: 13537-13542, 2003. (Pubitemid 37444777)
24. Perumal SS, Shanthi P and Sachdanandam P. Therapeutic effect of tamoxifen and energy-modulating vitamins on carbohydrate-metabolizing enzymes in breast cancer. Cancer Chemother Pharmacol 56: 105-114, 2005. (Pubitemid 41201763)
25. Oikawa T and Yamada T. Molecular biology of the Ets family of transcription factors. Gene 303: 11-34, 2003. (Pubitemid 36151767)
26. Sankar S, Gomez NC, Bell R, Patel M, Davis IJ, Lessnick SL and Luo W. EWS and RE1-silencing transcription factor inhibit neuronal phenotype development and oncogenic transformation in Ewing sarcoma. Genes Cancer 4: 213-223, 2013.
27. Lüdtke TH, Farin HF, Rudat C, Schuster-Gossler K, Petry M, Barnett P, Christoffels VM and Kispert A. Tbx2 controls lung growth by direct repression of the cell cycle inhibitor genes Cdkn1a and Cdkn1b. PLoS Genet 9: e1003189, 2013.
28. Cazzalini O, Scovassi AI, Savio M, Stivala LA and Prosperi E. Multiple roles of the cell cycle inhibitor p21(CDKN1A) in the DNA damage response. Mutat Res 704: 12-20, 2010.
29. Choudhury AR, Ju Z, Djojosubroto MW, Schienke A, Lechel A, Schaetzlein S, Jiang H, Stepczynska A, Wang C, Buer J, et al: Cdkn1a deletion improves stem cell function and lifespan of mice with dysfunctional telomeres without accelerating cancer formation. Nat Genet 39: 99-105, 2007. (Pubitemid 46026508)
30. Schwentner R: Molecular mechanisms of transcriptional repression by the EWS-FLI1 oncogene in Ewing's sarcoma. PhD dissertation, University of Vienna. Publication no. AC07884381, 2008.
31. Riggi N, Cironi L, Provero P, Suvà ML, Kaloulis K, Garcia-Echeverria C, Hoffmann F, Trumpp A and Stamenkovic I: Development of Ewing's sarcoma from primary bone marrow-derived mesenchymal progenitor cells. Cancer Res 65: 11459-11468, 2005. (Pubitemid 41821703)
32. Liu AY, Corey E, Vessella RL, Lange PH, True LD, Huang GM, Nelson PS and Hood L: Identification of differentially expressed prostate genes: increased expression of transcription factor ETS-2 in prostate cancer. Prostate 30: 145-153, 1997. (Pubitemid 27149272)
33. Butticé G and Kurkinen M: Oncogenes control stromelysin and collagenase gene expression. Contrib Nephrol 107: 101-107, 1994.
34. Sudol M: From Rous sarcoma virus to plasminogen activator, src oncogene and cancer management. Oncogene 30: 3003-3010, 2011.
35. Watanabe T, Miura T, Degawa Y, Fujita Y, Inoue M, Kawaguchi M and Furihata C: Comparison of lung cancer cell lines representing four histopathological subtypes with gene expression profiling using quantitative real-time PCR. Cancer Cell Int 10: 2, 2010.
36. Ibanez de Caceres I, Dulaimi E, Hoffman AM, Al-Saleem T, Uzzo RG and Cairns P: Identification of novel target genes by an epigenetic reactivation screen of renal cancer. Cancer Res 66: 5021-5028, 2006. (Pubitemid 43844922)
37. Maness L, Goktepe I, Chen H, Ahmedna M and Sang S: Impact of Phytolacca americana extracts on gene expression of colon cancer cells. Phytother Res: Apr 4, 2013 (Epub ahead of print) doi: 10.1002/ptr.4979.
38. Cirillo G, Casalino L, Vallone D, Caracciolo A, De Cesare D and Verde P: Role of distinct mitogen-activated protein kinase pathways and cooperation between Ets-2, ATF-2, and Jun family members in human urokinase-type plasminogen activator gene induction by interleukin-1 and tetradecanoyl phorbol acetate. Mol Cell Biol 19: 6240-6252, 1999. (Pubitemid 29399328)
39. Gervasi M, Bianchi-Smiraglia A, Cummings M, Zheng Q, Wang D, Liu S and Bakin AV: JunB contributes to Id2 repression and the epithelial-mesenchymal transition in response to transforming growth factor-β. J Cell Biol 196: 589-603, 2012.
40. Yang MY, Liu TC, Chang JG, Lin PM and Lin SF: JunB gene expression is inactivated by methylation in chronic myeloid leukemia. Blood 101: 3205-3211, 2003.
41. Liu PL, Tsai JR, Hwang JJ, Chou SH, Cheng YJ, Lin FY, Chen YL, Hung CY, Chen WC, Chen YH and Chong IW: High-mobility group box 1-mediated matrix metalloproteinase-9 expression in non-small cell lung cancer contributes to tumor cell invasiveness. Am J Resp Cell Mol Biol 43: 530-538, 2010.
42. Sahin A, Vercamer C, Kaminski A, Fuchs T, Florin A, Hahne JC, Mattot V, Pourtier-Manzanedo A, Pietsch T, Fafeur V and Wernert N: Dominant-negative inhibition of Ets 1 suppresses tumor growth, invasion and migration in rat C6 glioma cells and reveals differentially expressed Ets 1 target genes. Int J Oncol 34: 377, 2009.
43. Cha ST, Chen PS, Johansson G, Chu CY, Wang MY, Jeng YM, Yu SL, Chen JS, Chang KJ, Jee SH, et al: MicroRNA-519c suppresses hypoxia-inducible factor-1 alpha expression and tumor angiogenesis. Cancer Res 70: 2675-2685, 2010.
44. Alexopoulou AN, Leao M, Caballero OL, Da Silva L, Reid L, Lakhani SR, Simpson AJ, Marshall JF, Neville AM and Jat PS: Dissecting the transcriptional networks underlying breast cancer: NR4A1 reduces the migration of normal and breast cancer cell lines. Breast Cancer Res 12: R51, 2010.
45. Lee SO, Li X, Khan S and Safe S: Targeting NR4A1 (TR3) in cancer cells and tumors. Expert Opin Ther Targets 15: 195-206, 2011.
46. Robbins GT and Nie D: PPARgamma, bioactive lipids, and cancer progression. Front Biosci (Landmark Ed) 17: 1816-1834, 2012.
47. Clements A, Engle D, Shelton D, Neff T, Park S, Bender D, Ahmed A, De Geest K, Button A, Engelhardt JF and Goodheart M: Lymphoid Enhancing Factor 1 (Lef-1) overexpression in epithelial ovarian, fallopian tube and peritoneal cancer and associations with clinical factors. Proc Obstet Gynecol 2: 1-2, 2011.
48. Tomlins SA, Mehra R, Rhodes DR, Smith LR, Roulston D, Helgeson BE, Cao X, Wei JT, Rubin MA, Shah RB and Chinnaiyan AM: TMPRSS2: ETV4 gene fusions define a third molecular subtype of prostate cancer. Cancer Res 66: 3396-3400, 2006.
49. Darnell JE Jr: Transcription factors as targets for cancer therapy. Nat Rev Cancer 2: 740-749, 2002.