메뉴 건너뛰기




Volumn 8, Issue , 2007, Pages

A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments

Author keywords

[No Author keywords available]

Indexed keywords

EXPECTATION-MAXIMIZATION ALGORITHMS; GENE EXPRESSION DATA; HIGH-THROUGHPUT; MARKOV CHAIN MONTE CARLO; METASTATIC CANCERS; MICROARRAY EXPERIMENTS; MICROARRAY TECHNOLOGIES; PROBABILISTIC FRAMEWORK;

EID: 39549116496     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-364     Document Type: Article
Times cited : (49)

References (36)
  • 2
    • 0033557255 scopus 로고    scopus 로고
    • Meta-analysis: Formulating, Evaluating, Combining, and Reporting
    • 10.1002/(SICI)1097-0258(19990215)18:3<321::AID-SIM28>3.0.CO;2-P 10070677
    • Normand SLT: Meta-analysis: Formulating, Evaluating, Combining, and Reporting. Statistics in Medicine 1999, 18:321-359. 10.1002/ (SICI)1097-0258(19990215)18:3<321::AID-SIM28>3.0.CO;2-P 10070677
    • (1999) Statistics in Medicine , vol.18 , pp. 321-359
    • Normand, S.L.T.1
  • 3
    • 0036682376 scopus 로고    scopus 로고
    • Meta-Analysis of Microarrays: Interstudy Validation of Gene Expression Profiles Reveals Pathway Dysregulation in Prostate Cancer
    • 12154050
    • Rhodes D 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 Research 2002, 62:4427-33. 12154050
    • (2002) Cancer Research , vol.62 , pp. 4427-4433
    • Rhodes, D.1    Barrette, T.R.2    Rubin, M.A.3    Ghosh, D.4    Chinnaiyan, A.M.5
  • 4
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • 10.1111/1467-9868.00346
    • Storey JD: A direct approach to false discovery rates. J R Stat Soc B 2002, 64:479-98. 10.1111/1467-9868.00346
    • (2002) J R Stat Soc B , vol.64 , pp. 479-498
    • Storey, J.D.1
  • 5
    • 4944232237 scopus 로고    scopus 로고
    • Combining multiple microarray studies and modeling interstudy variation
    • 10.1093/bioinformatics/btg1010
    • Choi JK Yu U Kim S Yoo OJ; Combining multiple microarray studies and modeling interstudy variation. Bioinformatics 2003, 19:184-190. 10.1093/ bioinformatics/btg1010
    • (2003) Bioinformatics , vol.19 , pp. 184-190
    • Choi, J.K.1    Yu, U.2    Kim, S.3    Yoo, O.J.4
  • 6
    • 10244224128 scopus 로고    scopus 로고
    • Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: A meta-analysis of three microarray studies
    • 10.1093/bioinformatics/bth381 15231529
    • Wang J Coombes K Highsmith W Keating M Abruzzo L; Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: A meta-analysis of three microarray studies. Bioinformatics 2004, 20:3166-78. 10.1093/bioinformatics/bth381 15231529
    • (2004) Bioinformatics , vol.20 , pp. 3166-3178
    • Wang, J.1    Coombes, K.2    Highsmith, W.3    Keating, M.4    Abruzzo, L.5
  • 7
    • 0036433548 scopus 로고    scopus 로고
    • A statistical framework for expression-based molecular classification in cancer
    • 10.1111/1467-9868.00358
    • Parmigiani G Garrett ES Anbazhagan R Gabrielson E: A statistical framework for expression-based molecular classification in cancer. J R Stat Soc B 2002, 64:717-36. 10.1111/1467-9868.00358
    • (2002) J R Stat Soc B , vol.64 , pp. 717-736
    • Parmigiani, G.1    Garrett, E.S.2    Anbazhagan, R.3    Gabrielson, E.4
  • 8
    • 20044395334 scopus 로고    scopus 로고
    • Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data
    • 544889 15598354 10.1186/1471-2164-5-94
    • Shen R Ghosh D Chinnaiyan AM; Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data. BMC Genomics 2004, 5:94. 544889 15598354 10.1186/1471-2164-5-94
    • (2004) BMC Genomics , vol.5 , pp. 94
    • Shen, R.1    Ghosh, D.2    Chinnaiyan, A.M.3
  • 9
    • 0001677717 scopus 로고
    • Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
    • Benjamini Y Hochberg Y; Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J R Statist Soc Ser B 1995, 57:289-30.
    • (1995) J R Statist Soc Ser B , vol.57 , pp. 289-330
    • Benjamini, Y.1    Hochberg, Y.2
  • 10
    • 0036682002 scopus 로고    scopus 로고
    • Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease
    • 12154061
    • LaTulippe E Satagopan J Smith A Scher H Scardino P Reuter V Gerald WL: Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease. Cancer Res 2002, 62:4499-506. 12154061
    • (2002) Cancer Res , vol.62 , pp. 4499-4506
    • LaTulippe, E.1    Satagopan, J.2    Smith, A.3    Scher, H.4    Scardino, P.5    Reuter, V.6    Gerald, W.L.7
  • 13
    • 33747017793 scopus 로고    scopus 로고
    • Bayesian models for pooling microarray studies with multiple sources of replications
    • 1534062 16677390 10.1186/1471-2105-7-247
    • Conlon EM Song JJ Liu JS; Bayesian models for pooling microarray studies with multiple sources of replications. BMC Bioinformatics 2006, 7:247. 1534062 16677390 10.1186/1471-2105-7-247
    • (2006) BMC Bioinformatics , vol.7 , pp. 247
    • Conlon, E.M.1    Song, J.J.2    Liu, J.S.3
  • 15
    • 3042694117 scopus 로고    scopus 로고
    • Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
    • 438973 15184677 10.1073/pnas.0401994101
    • Rhodes D Yu J Shanker K Deshpande N Varambally R Ghosh D Barrette T Pandey A Chinnaiyan A; Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci USA 2004, 101:9309-14. 438973 15184677 10.1073/pnas.0401994101
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 9309-9314
    • Rhodes, D.1    Yu, J.2    Shanker, K.3    Deshpande, N.4    Varambally, R.5    Ghosh, D.6    Barrette, T.7    Pandey, A.8    Chinnaiyan, A.9
  • 17
  • 19
    • 33745220780 scopus 로고    scopus 로고
    • Met-regulated expression signature defines asubset of human hepatocellular carcinomas with poor prognosis and aggresive phenotype
    • 1462944 16710476 10.1172/JCI27236
    • Kaposi-Novak P Lee JS Gomez-Quiroz L Coulouarn C Factor VM Thorgeirsson SS; Met-regulated expression signature defines asubset of human hepatocellular carcinomas with poor prognosis and aggresive phenotype. Journal of Clinical Investigation 2006, 116:1582-1595. 1462944 16710476 10.1172/JCI27236
    • (2006) Journal of Clinical Investigation , vol.116 , pp. 1582-1595
    • Kaposi-Novak, P.1    Lee, J.S.2    Gomez-Quiroz, L.3    Coulouarn, C.4    Factor, V.M.5    Thorgeirsson, S.S.6
  • 20
    • 26444568601 scopus 로고    scopus 로고
    • Genes involved in invasion and metastasis of gastric cancer identified by array-based hybridization and serial analysis of gene expression
    • 10.1159/000086627 16210872
    • Oue N Aung PP Mitani Y Kuniyasu H Nakayama H Yasui W; Genes involved in invasion and metastasis of gastric cancer identified by array-based hybridization and serial analysis of gene expression. Oncology 2005, 69:17-22. 10.1159/000086627 16210872
    • (2005) Oncology , vol.69 , pp. 17-22
    • Oue, N.1    Aung, P.P.2    Mitani, Y.3    Kuniyasu, H.4    Nakayama, H.5    Yasui, W.6
  • 21
    • 33846455463 scopus 로고    scopus 로고
    • Gene expression profiling reveals a massive aneuploidy-dependent transcriptional deregulation and distinct differences between lymph node-negative and lymph node-positive colon carcinomas
    • 10.1158/0008-5472.CAN-06-1514 17210682
    • Grade M Hormann P Becker S Hummon AB Wangsa D Varma S Simon R Liersch T Becker H Difilippantonio MJ Ghadimi M Ried T; Gene expression profiling reveals a massive aneuploidy-dependent transcriptional deregulation and distinct differences between lymph node-negative and lymph node-positive colon carcinomas. Cancer Research 2007, 67:41-56. 10.1158/ 0008-5472.CAN-06-1514 17210682
    • (2007) Cancer Research , vol.67 , pp. 41-56
    • Grade, M.1    Hormann, P.2    Becker, S.3    Hummon, A.B.4    Wangsa, D.5    Varma, S.6    Simon, R.7    Liersch, T.8    Becker, H.9    Difilippantonio, M.J.10    Ghadimi, M.11    Ried, T.12
  • 22
    • 0000336139 scopus 로고
    • Regression models and life tables (with discussion)
    • Cox DR: Regression models and life tables (with discussion). J R Statist Soc Ser B 1972, 34:187-220.
    • (1972) J R Statist Soc Ser B , vol.34 , pp. 187-220
    • Cox, D.R.1
  • 23
    • 0030069896 scopus 로고    scopus 로고
    • Multivariable prognostic models: Issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors
    • 10.1002/(SICI)1097-0258(19960229)15:4<361::AID-SIM168>3.0.CO;2-4 8668867
    • Harrell FE Lee KL Mark DB: Iultivariable prognostic models: issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors. Stat Med 1996, 15:361-387. 10.1002/ (SICI)1097-0258(19960229)15:4<361::AID-SIM168>3.0.CO;2-4 8668867
    • (1996) Stat Med , vol.15 , pp. 361-387
    • Harrell, F.E.1    Lee, K.L.2    Mark, D.B.3
  • 25
    • 2442545413 scopus 로고    scopus 로고
    • A cross-study comparison of gene expression studies for the molecular classification of lung cancer
    • 10.1158/1078-0432.CCR-03-0490 15131026
    • Parmigiani G Garrett-Meyer ES Anbazhagan R Gabrielson E; A cross-study comparison of gene expression studies for the molecular classification of lung cancer. Clin Cancer Res 2004, 10:2922-7. 10.1158/ 1078-0432.CCR-03-0490 15131026
    • (2004) Clin Cancer Res , vol.10 , pp. 2922-2927
    • Parmigiani, G.1    Garrett-Meyer, E.S.2    Anbazhagan, R.3    Gabrielson, E.4
  • 26
    • 84886767298 scopus 로고    scopus 로고
    • metaArray http://www.bioconductor.org/packages/2.0/bioc/html/ metaArray.html
    • MetaArray
  • 27
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • Yang YH Dudoit S Luu P Lin DM Peng V Ngai J Speed TP: Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 2002, 30:eL5.
    • (2002) Nucleic Acids Research , vol.30
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5    Ngai, J.6    Speed, T.P.7
  • 28
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • 10.1093/biostatistics/4.2.249 12925520
    • 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. 10.1093/biostatistics/4.2.249 12925520
    • (2003) Biostatistics , vol.4 , pp. 249-264
    • Irizarry, R.A.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.D.4    Antonellis, K.J.5    Scherf, U.6    Speed, T.P.7
  • 29
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to ionizing radiation response
    • 33173 11309499 10.1073/pnas.091062498
    • Tusher VG Tibshirani R Chu G; Significance analysis of microarrays applied to ionizing radiation response. Proc Natl Acad Sci 2001, 98:5116-21. 33173 11309499 10.1073/pnas.091062498
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 30
    • 25444500666 scopus 로고    scopus 로고
    • Normal uniform mixture differential gene expression detection for cDNA microarrays
    • 1181627 16011807 10.1186/1471-2105-6-173
    • Dean N Raftery AE: Normal uniform mixture differential gene expression detection for cDNA microarrays. BMC Bioinformatics 2005, 6:173. 1181627 16011807 10.1186/1471-2105-6-173
    • (2005) BMC Bioinformatics , vol.6 , pp. 173
    • Dean, N.1    Raftery, A.E.2
  • 32
    • 0037336570 scopus 로고    scopus 로고
    • Statistical modeling and visualization of molecular profiles in cancer
    • Scharpf R Garrett ES Hu J Parmigiani G; Statistical modeling and visualization of molecular profiles in cancer. BioTechniques 2003, 34:S22-S29.
    • (2003) BioTechniques , vol.34
    • Scharpf, R.1    Garrett, E.S.2    Hu, J.3    Parmigiani, G.4
  • 33
    • 13244258379 scopus 로고    scopus 로고
    • Tests for finding complex patterns of differential expression in cancers: Towards individualized medicine
    • 514539 15307894 10.1186/1471-2105-5-110
    • Lyons-Weiler J Patel S Becich MJ Godfrey T; Tests for finding complex patterns of differential expression in cancers: Towards individualized medicine. BMC Bioinformatics 2004, 5:110. 514539 15307894 10.1186/ 1471-2105-5-110
    • (2004) BMC Bioinformatics , vol.5 , pp. 110
    • Lyons-Weiler, J.1    Patel, S.2    Becich, M.J.3    Godfrey, T.4
  • 34
    • 4444235995 scopus 로고    scopus 로고
    • Detecting differential gene expression with a semiparametric hierarchical mixture method
    • 10.1093/biostatistics/5.2.155 15054023
    • Newton MA Noueiry A Sarkar D Ahlquist P; Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 2004, 5:155-176. 10.1093/biostatistics/5.2.155 15054023
    • (2004) Biostatistics , vol.5 , pp. 155-176
    • Newton, M.A.1    Noueiry, A.2    Sarkar, D.3    Ahlquist, P.4
  • 35
    • 0346888587 scopus 로고    scopus 로고
    • On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles
    • 10.1002/sim.1548 14673946
    • Kendziorski CM Newton MA Lan H Gould MN; On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Stat Med 2003, 22:3899-3914. 10.1002/sim.1548 14673946
    • (2003) Stat Med , vol.22 , pp. 3899-3914
    • Kendziorski, C.M.1    Newton, M.A.2    Lan, H.3    Gould, M.N.4
  • 36
    • 0027304920 scopus 로고
    • Tightening the Clinical Trial
    • 10.1016/0197-2456(93)90225-3 8365193
    • Tukey JW: Tightening the Clinical Trial. Controlled Clinical Trials 1993, 14:266-285. 10.1016/0197-2456(93)90225-3 8365193
    • (1993) Controlled Clinical Trials , vol.14 , pp. 266-285
    • Tukey, J.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.