Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior

Acta Veterinaria Scandinavica

Volumn 53, Issue 1, 2011, Pages

  Tsoi, Lam C ^a   Qin, Tingting ^a   Slate, Elizabeth H ^b   Zheng, W Jim ^a  

^a MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIFFERENTIAL EXPRESSIONS; FALSE DISCOVERY RATE; HETEROGENEOUS DATASETS; MICROARRAY DATASET; MICROARRAY EXPERIMENTS; SIMULATION STUDIES; TRANSCRIPTION PROFILES; VESSEL DEVELOPMENT;

BLOOD VESSELS; COMPUTER SIMULATION; DISEASES; ERROR ANALYSIS;

GENE EXPRESSION;

ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; META ANALYSIS (TOPIC); METASTASIS; METHODOLOGY;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; META-ANALYSIS AS TOPIC; NEOPLASM METASTASIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 84855475302     PISSN: 0044605X     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-12-438     Document Type: Article

References (53)

1. Barrett T, Edgar R. Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. Methods Mol Biol 2006, 338:175-190. 1619899, 16888359.
2. Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003, 31(1):68-71. 10.1093/nar/gkg091, 165538, 12519949.
3. Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. The Stanford Microarray Database. Nucleic Acids Res 2001, 29(1):152-155. 10.1093/nar/29.1.152, 29818, 11125075.
4. Ghosh D, Barette TR, Rhodes D, Chinnaiyan AM. Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics 2003, 3(4):180-188. 10.1007/s10142-003-0087-5, 12884057.
5. Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 2002, 62(15):4427-4433.
6. Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M. Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet 2003, 19(10):570-577. 10.1016/j.tig.2003.08.006, 14550631.
7. Conlon EM. A Bayesian mixture model for metaanalysis of microarray studies. Funct Integr Genomics 2008, 8(1):43-53. 10.1007/s10142-007-0058-3, 17879102.
8. Conlon EM, Song JJ, Liu JS. Bayesian models for pooling microarray studies with multiple sources of replications. BMC Bioinformatics 2006, 7:247. 10.1186/1471-2105-7-247, 1534062, 16677390.
9. Shen R, Ghosh D, Chinnaiyan AM. Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data. BMC Genomics 2004, 5(1):94. 10.1186/1471-2164-5-94, 544889, 15598354.
10. Breitling R, Armengaud P, Amtmann A, Herzyk P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 2004, 573(1-3):83-92. 10.1016/j.febslet.2004.07.055, 15327980.
11. Kong X, Mas V, Archer KJ. A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy. BMC Genomics 2008, 9:98. 10.1186/1471-2164-9-98, 2276496, 18302764.
12. Cahan P, Rovegno F, Mooney D, Newman JC, St Laurent G, McCaffrey TA. Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. Gene 2007, 401(1-2):12-18. 10.1016/j.gene.2007.06.016, 2111172, 17651921.
13. Boedigheimer MJ, Wolfinger RD, Bass MB, Bushel PR, Chou JW, Cooper M, Corton JC, Fostel J, Hester S, Lee JS, Liu F, Liu J, Qian HR, Quackenbush J, Pettit S, Thompson KL. Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories. BMC Genomics 2008, 9:285. 10.1186/1471-2164-9-285, 2453529, 18549499.
14. Hong F, Breitling R. A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics 2008, 24(3):374-382. 10.1093/bioinformatics/btm620, 18204063.
15. Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics 2006, 22(22):2825-2827. 10.1093/bioinformatics/btl476, 16982708.
16. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci USA 2004, 101(25):9309-9314. 10.1073/pnas.0401994101, 438973, 15184677.
17. Pawitan Y, Michiels S, Koscielny S, Gusnanto A, Ploner A. False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 2005, 21(13):3017-3024. 10.1093/bioinformatics/bti448, 15840707.
18. Ma S, Huang J. Regularized gene selection in cancer microarray meta-analysis. BMC Bioinformatics 2009, 10:1. 10.1186/1471-2105-10-1, 2631520, 19118496.
19. Rhodes DR, Chinnaiyan AM. Bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers. Ann N Y Acad Sci 2004, 1020:32-40. 10.1196/annals.1310.005, 15208181.
20. Culhane AC, Quackenbush J. Confounding effects in "A six-gene signature predicting breast cancer lung metastasis". Cancer Res 2009, 69(18):7480-7485. 10.1158/0008-5472.CAN-08-3350, 3128918, 19723662.
21. Rhodes DR, Chinnaiyan AM. Integrative analysis of the cancer transcriptome. Nat Genet 2005, 37(Suppl):S31-37.
22. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
23. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003, 100(16):9440-9445. 10.1073/pnas.1530509100, 170937, 12883005.
24. Thomas A, Hara BO, Ligges U, Sturtz S. Making BUGS Open. R News 2006, 6:12-17.
25. Lunn DJ, Thomas A, Best N, Spiegelhalter D. WinBUGS--a Bayesian modelling framework: concepts, structure, and extensibility. Statistics and Computing 2000, 10:325-337.
26. Lunn DJ, Spiegelhalter D, Thomas A, Best N. The BUGS project: Evolution, critique and future directions. Statistics in Medicine 2009, 28:3049-3082. 10.1002/sim.3680, 19630097.
27. Zhang S. A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance. BMC Bioinformatics 2007, 8:230. 10.1186/1471-2105-8-230, 1955751, 17603887.
28. Bachtiary B, Boutros PC, Pintilie M, Shi W, Bastianutto C, Li JH, Schwock J, Zhang W, Penn LZ, Jurisica I, Fyles A, Liu FF. Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity. Clin Cancer Res 2006, 12(19):5632-5640. 10.1158/1078-0432.CCR-06-0357, 17020965.
29. Chandran UR, Ma C, Dhir R, Bisceglia M, Lyons-Weiler M, Liang W, Michalopoulos G, Becich M, Monzon FA. Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process. BMC Cancer 2007, 7:64. 10.1186/1471-2407-7-64, 1865555, 17430594.
30. Hippo Y, Taniguchi H, Tsutsumi S, Machida N, Chong JM, Fukayama M, Kodama T, Aburatani H. Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res 2002, 62(1):233-240.
31. O'Donnell RK, Kupferman M, Wei SJ, Singhal S, Weber R, O'Malley B, Cheng Y, Putt M, Feldman M, Ziober B, Muschel RJ. Gene expression signature predicts lymphatic metastasis in squamous cell carcinoma of the oral cavity. Oncogene 2005, 24(7):1244-1251. 10.1038/sj.onc.1208285, 15558013.
32. Provenzani A, Fronza R, Loreni F, Pascale A, Amadio M, Quattrone A. Global alterations in mRNA polysomal recruitment in a cell model of colorectal cancer progression to metastasis. Carcinogenesis 2006, 27(7):1323-1333. 10.1093/carcin/bgi377, 16531451.
33. Yu YP, Landsittel D, Jing L, Nelson J, Ren B, Liu L, McDonald C, Thomas R, Dhir R, Finkelstein S, Michalopoulos G, Becich M, Luo JH. Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J Clin Oncol 2004, 22(14):2790-2799. 10.1200/JCO.2004.05.158, 15254046.
34. Jones J, Otu H, Spentzos D, Kolia S, Inan M, Beecken WD, Fellbaum C, Gu X, Joseph M, Pantuck AJ, Jonas D, Libermann TA. Gene signatures of progression and metastasis in renal cell cancer. Clin Cancer Res 2005, 11(16):5730-5739. 10.1158/1078-0432.CCR-04-2225, 16115910.
35. 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(2):249-264. 10.1093/biostatistics/4.2.249, 12925520.
36. Rose AA, Pepin F, Russo C, Abou Khalil JE, Hallett M, Siegel PM. Osteoactivin promotes breast cancer metastasis to bone. Mol Cancer Res 2007, 5(10):1001-1014. 10.1158/1541-7786.MCR-07-0119, 17951401.
37. Denhardt DT, Mistretta D, Chambers AF, Krishna S, Porter JF, Raghuram S, Rittling SR. Transcriptional regulation of osteopontin and the metastatic phenotype: evidence for a Ras-activated enhancer in the human OPN promoter. Clin Exp Metastasis 2003, 20(1):77-84. 10.1023/A:1022550721404, 12650610.
38. Takami Y, Russell MB, Gao C, Mi Z, Guo H, Mantyh CR, Kuo PC. Sp1 regulates osteopontin expression in SW480 human colon adenocarcinoma cells. Surgery 2007, 142(2):163-169. 10.1016/j.surg.2007.02.015, 2174430, 17689681.
39. Takafuji V, Forgues M, Unsworth E, Goldsmith P, Wang XW. An osteopontin fragment is essential for tumor cell invasion in hepatocellular carcinoma. Oncogene 2007, 26(44):6361-6371. 10.1038/sj.onc.1210463, 17452979.
40. Tang H, Wang J, Bai F, Zhai H, Gao J, Hong L, Xie H, Zhang F, Lan M, Yao W, Liu J, Wu K, Fan D. Positive correlation of osteopontin, cyclooxygenase-2 and vascular endothelial growth factor in gastric cancer. Cancer Invest 2008, 26(1):60-67. 10.1080/07357900701519279, 18181047.
41. Lee DY, Park CS, Kim HS, Kim JY, Kim YC, Lee S. Maspin and p53 protein expression in gastric adenocarcinoma and its clinical applications. Appl Immunohistochem Mol Morphol 2008, 16(1):13-18.
42. Ma Y, Peng ZL. [Expression of maspin and its relation to tumor vascularization in epithelian ovarian cancer]. Sichuan Da Xue Xue Bao Yi Xue Ban 2009, 40(2):223-227.
43. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
44. Weinberg RA. The biology of cancer. 2007, New York: Garland Science.
45. Ono T, Sekino-Suzuki N, Kikkawa Y, Yonekawa H, Kawashima S. Alivin 1, a novel neuronal activity-dependent gene, inhibits apoptosis and promotes survival of cerebellar granule neurons. J Neurosci 2003, 23(13):5887-5896.
46. Kuja-Panula J, Kiiltomaki M, Yamashiro T, Rouhiainen A, Rauvala H. AMIGO, a transmembrane protein implicated in axon tract development, defines a novel protein family with leucine-rich repeats. J Cell Biol 2003, 160(6):963-973. 10.1083/jcb.200209074, 2173769, 12629050.
47. Piddini E, Schmid JA, de Martin R, Dotti CG. The Ras-like GTPase Gem is involved in cell shape remodelling and interacts with the novel kinesin-like protein KIF9. EMBO J 2001, 20(15):4076-4087. 10.1093/emboj/20.15.4076, 149163, 11483511.
48. Splingard A, Menetrey J, Perderiset M, Cicolari J, Regazzoni K, Hamoudi F, Cabanie L, El Marjou A, Wells A, Houdusse A, de Gunzburg J. Biochemical and structural characterization of the gem GTPase. J Biol Chem 2007, 282(3):1905-1915.
49. Hall A. The cytoskeleton and cancer. Cancer Metastasis Rev 2009, 28(1-2):5-14. 10.1007/s10555-008-9166-3, 19153674.
50. Lasagni L, Francalanci M, Annunziato F, Lazzeri E, Giannini S, Cosmi L, Sagrinati C, Mazzinghi B, Orlando C, Maggi E, Marra F, Romagnani S, Serio M, Romagnani P. An alternatively spliced variant of CXCR3 mediates the inhibition of endothelial cell growth induced by IP-10, Mig, and I-TAC, and acts as functional receptor for platelet factor 4. J Exp Med 2003, 197(11):1537-1549. 10.1084/jem.20021897, 2193908, 12782716.
51. Affymetrix Statistical Algorithms Description Document. 2002, Santa Clara: Affymetrix, Affymetrix.
52. Stevens JR, Doerge RW. Meta-analysis combines affymetrix microarray results across laboratories. Comp Funct Genomics 2005, 6(3):116-122. 10.1002/cfg.460, 2447518, 18629222.
53. Choi JK, Yu U, Kim S, Yoo OJ. Combining multiple microarray studies and modeling interstudy variation. Bioinformatics 2003, 19(Suppl 1):i84-90. 10.1093/bioinformatics/btg1010, 12855442.