메뉴 건너뛰기




Volumn 9, Issue , 2008, Pages

Combining transcriptional datasets using the generalized singular value decomposition

Author keywords

[No Author keywords available]

Indexed keywords

EXPERIMENTAL CONDITIONS; EXPRESSION MEASUREMENTS; GENE EXPRESSION DATASETS; GENERALIZED SINGULAR VALUE DECOMPOSITION; LARGE-SCALE STUDIES; MICROARRAY DATA SETS; QUANTITATIVE REAL TIME PCR; TRANSCRIPTIONAL LEVELS;

EID: 53549110812     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-335     Document Type: Article
Times cited : (12)

References (55)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary-DNA microarray
    • 7569999
    • Schena M Shalon D Davis RW Brown PO Quantitative monitoring of gene expression patterns with a complementary-DNA microarray Science 1995, 270:467-470 7569999
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 8
    • 33646052085 scopus 로고    scopus 로고
    • Pooling information across different studies and oligonucleotide microarray chip types to identify prognostic genes for lung cancer
    • New York: Springer-Verlag Shoemaker JS, Lin SM
    • Morris JS Yin G Baggerly KA Wu C Zhang L Pooling information across different studies and oligonucleotide microarray chip types to identify prognostic genes for lung cancer Methods of Microarray Data Analysis IV New York: Springer-Verlag Shoemaker JS, Lin SM 2005:51-66
    • (2005) Methods of Microarray Data Analysis IV , pp. 51-66
    • Morris, J.S.1    Yin, G.2    Baggerly, K.A.3    Wu, C.4    Zhang, L.5
  • 9
    • 33747874717 scopus 로고    scopus 로고
    • Combining multiple microarrays in the presence of controlling variables
    • 16705015
    • Park T Yi SG Shin YK Lee S Combining multiple microarrays in the presence of controlling variables Bioinformatics 2006, 22:1682-1689 16705015
    • (2006) Bioinformatics , vol.22 , pp. 1682-1689
    • Park, T.1    Yi, S.G.2    Shin, Y.K.3    Lee, S.4
  • 10
    • 0037221729 scopus 로고    scopus 로고
    • Dysregulation of the Annexin Family Protein Family Is Associated with Prostate Cancer Progression
    • 1851111 12507908
    • Xin W Rhodes DR Ingold C Chinnaiyan AM Rubin MA Dysregulation of the Annexin Family Protein Family Is Associated with Prostate Cancer Progression Am J Pathol 2003, 162(1):255-261 1851111 12507908
    • (2003) Am J Pathol , vol.162 , Issue.1 , pp. 255-261
    • Xin, W.1    Rhodes, D.R.2    Ingold, C.3    Chinnaiyan, A.M.4    Rubin, M.A.5
  • 11
    • 4944232237 scopus 로고    scopus 로고
    • Combining multiple microarray studies and modeling inter-study variation
    • 10.1093/bioinformatics/btg1010 12855442
    • Choi JK Yu U Kim S Yoo OJ Combining multiple microarray studies and modeling inter-study variation Bioinformatics 2003, 19:i84-i90 10.1093/ bioinformatics/btg1010 12855442
    • (2003) Bioinformatics , vol.19
    • Choi, J.K.1    Yu, U.2    Kim, S.3    Yoo, O.J.4
  • 12
    • 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
    • 15231529
    • Wang J Coombes KR Highsmith WE Keating MJ Abruzzo LV Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: A meta-analysis of three microarray studies Bioinformatics 2004, 20:3166-3178 15231529
    • (2004) Bioinformatics , vol.20 , pp. 3166-3178
    • Wang, J.1    Coombes, K.R.2    Highsmith, W.E.3    Keating, M.J.4    Abruzzo, L.V.5
  • 14
    • 2442545413 scopus 로고    scopus 로고
    • A cross-study comparison of gene expression studies for the molecular classification of lung cancer
    • 15131026
    • Parmigiani G Garrett-Mayer ES Anbazhagan R Gabrielson E A cross-study comparison of gene expression studies for the molecular classification of lung cancer Clinical Cancer Research 2004, 10:2922-2927 15131026
    • (2004) Clinical Cancer Research , vol.10 , pp. 2922-2927
    • Parmigiani, G.1    Garrett-Mayer, E.S.2    Anbazhagan, R.3    Gabrielson, E.4
  • 15
    • 13244289883 scopus 로고    scopus 로고
    • Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes
    • 476733 15217521
    • Jiang H Deng Y Chen H Tao L Sha Q Chen J Tsai C Zhang S Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes BMC Bioinformatics 2004, 5:81 476733 15217521
    • (2004) BMC Bioinformatics , vol.5 , pp. 81
    • Jiang, H.1    Deng, Y.2    Chen, H.3    Tao, L.4    Sha, Q.5    Chen, J.6    Tsai, C.7    Zhang, S.8
  • 16
    • 25444521278 scopus 로고    scopus 로고
    • Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
    • 1173085 15921507
    • Hu P Greenwood CMT Beyene J Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models BMC Bioinformatics 2005, 6:128 1173085 15921507
    • (2005) BMC Bioinformatics , vol.6 , pp. 128
    • Hu, P.1    Greenwood, C.M.T.2    Beyene, J.3
  • 17
    • 28944444652 scopus 로고    scopus 로고
    • Differential coexpression analysis using microarray data and its application to human cancer
    • 16234317
    • Choi JK Yu U Yoo OJ Kim S Differential coexpression analysis using microarray data and its application to human cancer Bioinformatics 2005, 21:4348-4355 16234317
    • (2005) Bioinformatics , vol.21 , pp. 4348-4355
    • Choi, J.K.1    Yu, U.2    Yoo, O.J.3    Kim, S.4
  • 18
    • 0036682376 scopus 로고    scopus 로고
    • Meta-analysis of microarrays: Inter-study validation of gene expression profiles reveals pathway dysregulation in prostate cancer
    • 12154050
    • Rhodes DR Barrette TR Rubin MA Ghosh D Chinnaiyan AM Meta-analysis of microarrays: Inter-study validation of gene expression profiles reveals pathway dysregulation in prostate cancer Cancer Research 2002, 62:4427-4433 12154050
    • (2002) Cancer Research , vol.62 , pp. 4427-4433
    • Rhodes, D.R.1    Barrette, T.R.2    Rubin, M.A.3    Ghosh, D.4    Chinnaiyan, A.M.5
  • 19
    • 3042694117 scopus 로고    scopus 로고
    • Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
    • 438973 15184677
    • 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, 101:9309-9314 438973 15184677
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 9309-9314
    • Rhodes, D.R.1    Yu, J.2    Shanker, K.3    Deshpande, N.4    Varambally, R.5    Ghosh, D.6    Barrette, T.7    Pandey, A.8    Chinnaiyan, A.M.9
  • 20
    • 34147103409 scopus 로고    scopus 로고
    • Bayesian meta-analysis models for microarray data: A comparative study
    • 1851021 17343745
    • Conlon EM Song JJ Liu A Bayesian meta-analysis models for microarray data: A comparative study BMC Bioinformatics 2007, 8:80 1851021 17343745
    • (2007) BMC Bioinformatics , vol.8 , pp. 80
    • Conlon, E.M.1    Song, J.J.2    Liu, A.3
  • 25
    • 0036773278 scopus 로고    scopus 로고
    • Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays
    • 12377987
    • Li J Pankratz M Johnson JA Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays Toxicol Sci 2002, 69:383-390 12377987
    • (2002) Toxicol Sci , vol.69 , pp. 383-390
    • Li, J.1    Pankratz, M.2    Johnson, J.A.3
  • 26
    • 0036211063 scopus 로고    scopus 로고
    • Analysis of matched mRNA measurements from two different microarray technologies
    • 11934739
    • Kuo WP Jenssen TK Butte AJ Ohno-Machado L Kohane IS Analysis of matched mRNA measurements from two different microarray technologies Bioinformatics 2002, 18:405-412 11934739
    • (2002) Bioinformatics , vol.18 , pp. 405-412
    • Kuo, W.P.1    Jenssen, T.K.2    Butte, A.J.3    Ohno-Machado, L.4    Kohane, I.S.5
  • 27
    • 0346670079 scopus 로고    scopus 로고
    • Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epithelium cell lines
    • 14551534
    • Rogojina AT Orr WE Song BK Geisert EE Jr Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epithelium cell lines Mol Vis 2003, 9:482-496 14551534
    • (2003) Mol Vis , vol.9 , pp. 482-496
    • Rogojina, A.T.1    Orr, W.E.2    Song, B.K.3    Geisert Jr., E.E.4
  • 30
    • 17844379157 scopus 로고    scopus 로고
    • A Comparison of cDNA, Oligonucleotide, and Affymetrix GeneChip Gene Expression Microarray Platforms
    • 2291701 15585824
    • Woo Y Affourtit J Daigle S Viale A Johnson K Naggert J Churchill G A Comparison of cDNA, Oligonucleotide, and Affymetrix GeneChip Gene Expression Microarray Platforms J Biomol Tech 2004, 15:276-284 2291701 15585824
    • (2004) J Biomol Tech , vol.15 , pp. 276-284
    • Woo, Y.1    Affourtit, J.2    Daigle, S.3    Viale, A.4    Johnson, K.5    Naggert, J.6    Churchill, G.7
  • 31
    • 7444234286 scopus 로고    scopus 로고
    • Getting the Noise Out of Gene Arrays
    • 15499004
    • Marshall E Getting the Noise Out of Gene Arrays Science 2004, 306:630-631 15499004
    • (2004) Science , vol.306 , pp. 630-631
    • Marshall, E.1
  • 32
    • 0037095769 scopus 로고    scopus 로고
    • Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays
    • 115302 12000853
    • Yuen T Wurmbach E Pfeffer RL Ebersole BJ Sealfon SC Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays Nucleic Acids Res 2002, 30:e48 115302 12000853
    • (2002) Nucleic Acids Res , vol.30
    • Yuen, T.1    Wurmbach, E.2    Pfeffer, R.L.3    Ebersole, B.J.4    Sealfon, S.C.5
  • 34
    • 31444431754 scopus 로고    scopus 로고
    • Reliability and reproducibility issues in DNA microarray measurements
    • 2386979 16380191
    • Draghici S Khatri P Eklund AC Zoltan S Reliability and reproducibility issues in DNA microarray measurements Trends Genet 2006, 22:101-109 2386979 16380191
    • (2006) Trends Genet , vol.22 , pp. 101-109
    • Draghici, S.1    Khatri, P.2    Eklund, A.C.3    Zoltan, S.4
  • 36
    • 34948882332 scopus 로고    scopus 로고
    • A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences
    • 2000902 17708771
    • Lee JC Stiles D Lu J Cam MC A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences BMC Genomics 2007, 8:284 2000902 17708771
    • (2007) BMC Genomics , vol.8 , pp. 284
    • Lee, J.C.1    Stiles, D.2    Lu, J.3    Cam, M.C.4
  • 37
    • 0016926423 scopus 로고
    • Generalizing the singular value decomposition
    • 10.1137/0713009
    • van Loan CF Generalizing the singular value decomposition SIAM J Numer Anal 1976, 13:76-83 10.1137/0713009
    • (1976) SIAM J Numer Anal , vol.13 , pp. 76-83
    • van Loan, C.F.1
  • 38
    • 0001129014 scopus 로고
    • Towards a generalized singular value decomposition
    • 10.1137/0718026
    • Paige CC Saunders MA Towards a generalized singular value decomposition SIAM J Numer Anal 1981, 18:398-405 10.1137/0718026
    • (1981) SIAM J Numer Anal , vol.18 , pp. 398-405
    • Paige, C.C.1    Saunders, M.A.2
  • 40
    • 0037452966 scopus 로고    scopus 로고
    • Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms
    • 152296 12631705
    • Alter O Brown PO Botstein D Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms Proc Natl Acad Sci USA 2003, 100:3351-3356 152296 12631705
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 3351-3356
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 41
    • 33144468540 scopus 로고    scopus 로고
    • Jointly analyzing gene expression and copy number data in breast cancer using data reduction models
    • 17048389
    • Berger JA Hautaniemi S Mitra SK Astola J Jointly analyzing gene expression and copy number data in breast cancer using data reduction models IEEE/ACM Trans Comput Biol Bioinform 2006, 3(1):2-16 17048389
    • (2006) IEEE/ACM Trans Comput Biol Bioinform , vol.3 , Issue.1 , pp. 2-16
    • Berger, J.A.1    Hautaniemi, S.2    Mitra, S.K.3    Astola, J.4
  • 42
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • 27718 10963673
    • Alter O Brown PO Botstein D Singular value decomposition for genome-wide expression data processing and modeling Proc Natl Acad Sci USA 2000, 97:10101-10106 27718 10963673
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 43
    • 2542430932 scopus 로고    scopus 로고
    • Singular value decomposition and principal component analysis
    • Norwell, MA: Kluwer Berrar DP, Dubitzky W, Granzow M
    • Wall ME Rechtsteiner A Rocha LM Singular value decomposition and principal component analysis A practical approach to microarray data analysis Norwell, MA: Kluwer Berrar DP, Dubitzky W, Granzow M 2003:91-109
    • (2003) A Practical Approach to Microarray Data Analysis , pp. 91-109
    • Wall, M.E.1    Rechtsteiner, A.2    Rocha, L.M.3
  • 44
    • 26444434267 scopus 로고    scopus 로고
    • (1,3;1,4)-β-D-Glucans in the cell walls of the Poales (sensu lato): An immunogold labeling study using a monoclonal antibody
    • Trethewey JAK Campbell LM Harris PJ (1,3;1,4)-β-D-Glucans in the cell walls of the Poales (sensu lato): An immunogold labeling study using a monoclonal antibody Am J Bot 2005, 92:1660-1674 http://www.amjbot.org/cgi/content/abstract/92/10/1660
    • (2005) Am J Bot , vol.92 , pp. 1660-1674
    • Trethewey, J.A.K.1    Campbell, L.M.2    Harris, P.J.3
  • 46
    • 33645145479 scopus 로고    scopus 로고
    • Plant cell wall biosynthesis: Genetic, biochemical and functional genomics approaches to the identification of key genes
    • 17177793
    • Farrokhi N Burton RA Brownfield L Hrmova M Wilson SM Bacic A Fincher GB Plant cell wall biosynthesis: Genetic, biochemical and functional genomics approaches to the identification of key genes Plant Biotechnol J 2006, 4(2):145-167 17177793
    • (2006) Plant Biotechnol J , vol.4 , Issue.2 , pp. 145-167
    • Farrokhi, N.1    Burton, R.A.2    Brownfield, L.3    Hrmova, M.4    Wilson, S.M.5    Bacic, A.6    Fincher, G.B.7
  • 48
    • 0842307342 scopus 로고    scopus 로고
    • The CesA Gene Family of Barley. Quantitative Analysis of Transcripts Reveals Two Groups of Co-Expressed Genes
    • 316302 14701917
    • Burton RA Shirley NJ King BJ Harvey AJ Fincher GB The CesA Gene Family of Barley. Quantitative Analysis of Transcripts Reveals Two Groups of Co-Expressed Genes Plant Physiol 2004, 134:224-236 316302 14701917
    • (2004) Plant Physiol , vol.134 , pp. 224-236
    • Burton, R.A.1    Shirley, N.J.2    King, B.J.3    Harvey, A.J.4    Fincher, G.B.5
  • 49
    • 48549094244 scopus 로고    scopus 로고
    • The Genetics and Transcriptional Profiles of the Cellulose Synthase-Like HvCslF Gene Family in Barley
    • 2287353 18258691
    • Burton RA Jobling SA Harvey AJ Shirley NJ Mather DE Bacic A Fincher GB The Genetics and Transcriptional Profiles of the Cellulose Synthase-Like HvCslF Gene Family in Barley Plant Physiol 2008, 146:1821-1833 2287353 18258691
    • (2008) Plant Physiol , vol.146 , pp. 1821-1833
    • Burton, R.A.1    Jobling, S.A.2    Harvey, A.J.3    Shirley, N.J.4    Mather, D.E.5    Bacic, A.6    Fincher, G.B.7
  • 52
    • 20444426256 scopus 로고    scopus 로고
    • Lipid microdomains - Plant membranes get organized
    • 15949758
    • Martin SW Glover BJ Davies JM Lipid microdomains - plant membranes get organized Trends Plant Sci 2005, 10:263-265 15949758
    • (2005) Trends Plant Sci , vol.10 , pp. 263-265
    • Martin, S.W.1    Glover, B.J.2    Davies, J.M.3
  • 53
    • 31344457271 scopus 로고    scopus 로고
    • Glycosylphosphatidylinositol-anchored proteins are required for cell wall synthesis and morphogenesis in Arabidopsis
    • 1087991 15772281
    • Gillmor CS Lukowitz W Brininstool G Sedbrook JC Hamann T Poindexter P Somerville C Glycosylphosphatidylinositol-anchored proteins are required for cell wall synthesis and morphogenesis in Arabidopsis Plant Cell 2005, 17:1128-1140 1087991 15772281
    • (2005) Plant Cell , vol.17 , pp. 1128-1140
    • Gillmor, C.S.1    Lukowitz, W.2    Brininstool, G.3    Sedbrook, J.C.4    Hamann, T.5    Poindexter, P.6    Somerville, C.7
  • 54
    • 0033499327 scopus 로고    scopus 로고
    • Cellulose Biosynthesis: Exciting Times for a Difficult Field of Study
    • 15012210
    • Delmer DP Cellulose Biosynthesis: Exciting Times for a Difficult Field of Study Annu Rev Plant Physiol Plant Mol Biol 1999, 50:245-276 15012210
    • (1999) Annu Rev Plant Physiol Plant Mol Biol , vol.50 , pp. 245-276
    • Delmer, D.P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.