-
1
-
-
0035032570
-
Statistical design and the analysis of gene expression microarray data
-
10.1017/S0016672301005055 11355567
-
Kerr M GA C Statistical design and the analysis of gene expression microarray data Genet Res 2001, 77(2):123-128. 10.1017/S0016672301005055 11355567
-
(2001)
Genet Res
, vol.77
, Issue.2
, pp. 123-128
-
-
Kerr, M.G.A.C.1
-
2
-
-
24144445705
-
Improved statistical tests for differential gene expression by shrinking variance components estimates
-
10.1093/biostatistics/kxh018 15618528
-
Cui X Hwang J Qiu J Blades N Churchill G Improved statistical tests for differential gene expression by shrinking variance components estimates Biostatistics 2005, 6:59-75. 10.1093/biostatistics/kxh018 15618528
-
(2005)
Biostatistics
, vol.6
, pp. 59-75
-
-
Cui, X.1
Hwang, J.2
Qiu, J.3
Blades, N.4
Churchill, G.5
-
3
-
-
22144490889
-
A note on joint versus gene-specific mixed model analysis of microarray gene expression data
-
10.1093/biostatistics/kxi001 15772098
-
Hoeschele I Li H A note on joint versus gene-specific mixed model analysis of microarray gene expression data Biostatistics 2005, 6(2):183-186. 10.1093/biostatistics/kxi001 15772098
-
(2005)
Biostatistics
, vol.6
, Issue.2
, pp. 183-186
-
-
Hoeschele, I.1
Li, H.2
-
4
-
-
1542318824
-
Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays
-
10.1155/S1110865704310036
-
Hero A Fleury G Mears A Swaroop A Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays EURASP Journal of Applied Signal Processing 2004, 1:43-52. 10.1155/S1110865704310036
-
(2004)
EURASP Journal of Applied Signal Processing
, vol.1
, pp. 43-52
-
-
Hero, A.1
Fleury, G.2
Mears, A.3
Swaroop, A.4
-
5
-
-
0033569406
-
Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
-
10.1126/science.286.5439.531 10521349
-
Golub T Slonim D Tamayo P Huard C Gaasenbeek M Mesirov J Coller H Loh M Downing J Caligiuri M Bloomfield C Lander E Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring Science 1999, 286(5439):531-537. 10.1126/science.286.5439.531 10521349
-
(1999)
Science
, vol.286
, Issue.5439
, pp. 531-537
-
-
Golub, T.1
Slonim, D.2
Tamayo, P.3
Huard, C.4
Gaasenbeek, M.5
Mesirov, J.6
Coller, H.7
Loh, M.8
Downing, J.9
Caligiuri, M.10
Bloomfield, C.11
Lander, E.12
-
6
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
24541 9843981 10.1073/pnas.95.25.14863
-
Eisen M Spellman P Brown P Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 24541 9843981 10.1073/pnas.95.25.14863
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, Issue.25
, pp. 14863-14868
-
-
Eisen, M.1
Spellman, P.2
Brown, P.3
Botstein, D.4
-
7
-
-
33747830882
-
Clustering microarray gene expression data using weighted Chinese restaurant process
-
10.1093/bioinformatics/btl284 16766561
-
Qin Z Clustering microarray gene expression data using weighted Chinese restaurant process Bioinformatics 2006, 22(16):1988-1997. 10.1093/ bioinformatics/btl284 16766561
-
(2006)
Bioinformatics
, vol.22
, Issue.16
, pp. 1988-1997
-
-
Qin, Z.1
-
8
-
-
34548784394
-
Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data
-
10.1093/bioinformatics/btm328 17586543
-
Zhu D Li Y Li H Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data Bioinformatics 2007, 23(17):2298-2305. 10.1093/bioinformatics/btm328 17586543
-
(2007)
Bioinformatics
, vol.23
, Issue.17
, pp. 2298-2305
-
-
Zhu, D.1
Li, Y.2
Li, H.3
-
9
-
-
27744448992
-
Network constrained clustering for gene microarray data
-
10.1093/bioinformatics/bti655 16141248
-
Zhu D Hero A Cheng H Khanna R Swaroop A Network constrained clustering for gene microarray data Bioinformatics 2005, 21(21):4014-4020. 10.1093/ bioinformatics/bti655 16141248
-
(2005)
Bioinformatics
, vol.21
, Issue.21
, pp. 4014-4020
-
-
Zhu, D.1
Hero, A.2
Cheng, H.3
Khanna, R.4
Swaroop, A.5
-
10
-
-
33244455951
-
Evolutionary conservation of expression profiles between human and mouse orthologous genes
-
10.1093/molbev/msj054 16280543
-
Liao B Zhang J Evolutionary conservation of expression profiles between human and mouse orthologous genes Mol Biol Evol 2006, 23(3):530-540. 10.1093/molbev/msj054 16280543
-
(2006)
Mol Biol Evol
, vol.23
, Issue.3
, pp. 530-540
-
-
Liao, B.1
Zhang, J.2
-
11
-
-
33746054504
-
An analysis of intra array repeat: The good, the bad and the noninformative
-
1501018 16753054
-
Elbez Y Farkash-Amar S Simon I An analysis of intra array repeat: The good, the bad and the noninformative BMC Genomics 2006, 7:136. 1501018 16753054
-
(2006)
BMC Genomics
, vol.7
-
-
Elbez, Y.1
Farkash-Amar, S.2
Simon, I.3
-
12
-
-
33644759290
-
Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling
-
1413912 16492768 10.1073/pnas.0511150103
-
Bourquin J Subramanian A Langebrake C Reinhardt D Bernard O Ballerini P Baruchel A Cave H Dastugue N Hasle H Kaspers G Lessard M Michaux L Vyas P Wering E Zwaan C Golub T Orkinar S Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling Proc Natl Acad Sci USA 2006, 103(9):3339-3344. 1413912 16492768 10.1073/pnas.0511150103
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.9
, pp. 3339-3344
-
-
Bourquin, J.1
Subramanian, A.2
Langebrake, C.3
Reinhardt, D.4
Bernard, O.5
Ballerini, P.6
Baruchel, A.7
Cave, H.8
Dastugue, N.9
Hasle, H.10
Kaspers, G.11
Lessard, M.12
Michaux, L.13
Vyas, P.14
Wering, E.15
Zwaan, C.16
Golub, T.17
Orkinar, S.18
-
13
-
-
1842631448
-
Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control
-
10.1089/153623104773547462 15107234
-
Yanai I Graur D Ophir R Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control OMICS 2004, 8:15-24. 10.1089/153623104773547462 15107234
-
(2004)
OMICS
, vol.8
, pp. 15-24
-
-
Yanai, I.1
Graur, D.2
Ophir, R.3
-
14
-
-
13444251367
-
Evolutionary significance of gene expression divergence
-
1859841 15716085 10.1016/j.gene.2004.11.034
-
Jordan I Marino-Ramirez L Koonin E Evolutionary significance of gene expression divergence Gene 2005, 345:119-126. 1859841 15716085 10.1016/ j.gene.2004.11.034
-
(2005)
Gene
, vol.345
, pp. 119-126
-
-
Jordan, I.1
Marino-Ramirez, L.2
Koonin, E.3
-
15
-
-
29144535372
-
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
-
10.1093/nar/gni179
-
Dai M Wang P Boyd A Kostov G Athey B Jones E Bunney W Myers R Speed T Akil H Watson S Meng F Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data Nucleic Acids Res 2006, 33(20):e175. 10.1093/nar/gni179
-
(2006)
Nucleic Acids Res
, vol.33
, Issue.20
-
-
Dai, M.1
Wang, P.2
Boyd, A.3
Kostov, G.4
Athey, B.5
Jones, E.6
Bunney, W.7
Myers, R.8
Speed, T.9
Akil, H.10
Watson, S.11
Meng, F.12
-
16
-
-
33847679625
-
Improved precision and accuracy for microarrays using updated probe set definitions
-
1805763 17288599
-
Sandberg R Larsson O Improved precision and accuracy for microarrays using updated probe set definitions BMC Bioinformatics 2007, 8:48. 1805763 17288599
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Sandberg, R.1
Larsson, O.2
-
17
-
-
33846986793
-
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips
-
1784106 17224057
-
Stalteri M Harrison A Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips BMC Bioinformatics 2007, 8:13. 1784106 17224057
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Stalteri, M.1
Harrison, A.2
-
18
-
-
33644853775
-
Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors
-
1383502 16505381 10.1073/pnas.0508214103
-
Akimoto M Cheng H Zhu D Brzezinski J Khanna R Filippova E Oh E Jing Y Linares J Brooks M Zareparsi S Mears A Hero A Glaser T Swaroop A Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors Proc Natl Acad Sci USA 2006, 103(10):3890-3895. 1383502 16505381 10.1073/pnas.0508214103
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.10
, pp. 3890-3895
-
-
Akimoto, M.1
Cheng, H.2
Zhu, D.3
Brzezinski, J.4
Khanna, R.5
Filippova, E.6
Oh, E.7
Jing, Y.8
Linares, J.9
Brooks, M.10
Zareparsi, S.11
Mears, A.12
Hero, A.13
Glaser, T.14
Swaroop, A.15
-
20
-
-
33745457512
-
Identifying genes important for spermatogonial stem cell self-renewal and survival
-
1480440 16740658 10.1073/pnas.0603332103
-
Oatley J Avarbock M Telaranta A Fearon D Brinster R Identifying genes important for spermatogonial stem cell self-renewal and survival Proc Natl Acad Sci USA 2006, 103(25):9524-9529. 1480440 16740658 10.1073/ pnas.0603332103
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.25
, pp. 9524-9529
-
-
Oatley, J.1
Avarbock, M.2
Telaranta, A.3
Fearon, D.4
Brinster, R.5
-
22
-
-
10844290766
-
A model-based background adjustment for oligonucleotide expression arrays
-
Wu J Irizarry R Gentleman R Murillo F Spencer F A model-based background adjustment for oligonucleotide expression arrays JASA 2004, 99(468):909-917.
-
(2004)
JASA
, vol.99
, Issue.468
, pp. 909-917
-
-
Wu, J.1
Irizarry, R.2
Gentleman, R.3
Murillo, F.4
Spencer, F.5
-
23
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
-
14539 11134512 10.1073/pnas.011404098
-
Li C Wong W Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection Proc Natl Acad Sci USA 2001, 98:31-36. 14539 11134512 10.1073/pnas.011404098
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.2
-
24
-
-
0035734382
-
Nrl is required for rod photoreceptor development
-
10.1038/ng774 11694879
-
Mears A Kondo M Swain P Takada Y Bush R Saunders T Sieving P Swaroop A Nrl is required for rod photoreceptor development Nat Genet 2001, 29(4):447-452. 10.1038/ng774 11694879
-
(2001)
Nat Genet
, vol.29
, Issue.4
, pp. 447-452
-
-
Mears, A.1
Kondo, M.2
Swain, P.3
Takada, Y.4
Bush, R.5
Saunders, T.6
Sieving, P.7
Swaroop, A.8
-
25
-
-
0001677717
-
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 Roy Stat Soc B Met 1995, 57:289-300.
-
(1995)
J Roy Stat Soc B Met
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
26
-
-
0026453108
-
Regulation of retinal cGMP cascade by phosducin in bovine rod photoreceptor cells. Interaction of phosducin and transducin
-
1334080
-
Lee R Ting T Lieberman B Tobias D Ho Y Regulation of retinal cGMP cascade by phosducin in bovine rod photoreceptor cells. Interaction of phosducin and transducin J Biol Chem 1992, 267(35):25104-25112. 1334080
-
(1992)
J Biol Chem
, vol.267
, Issue.35
, pp. 25104-25112
-
-
Lee, R.1
Ting, T.2
Lieberman, B.3
Tobias, D.4
Ho, Y.5
-
27
-
-
2442425295
-
Functional analysis of the rod photoreceptor cGMP phosphodiesterase alpha-subunit gene promoter: Nrl and Crx are required for full transcriptional activity
-
10.1074/jbc.M401864200 15001570
-
Pittler S Zhang Y Chen S Mears A Zack D Ren Z Swain P Yao S Swaroop A White J Functional analysis of the rod photoreceptor cGMP phosphodiesterase alpha-subunit gene promoter: Nrl and Crx are required for full transcriptional activity J Biol Chem 2004, 279(19):19800-19807. 10.1074/jbc.M401864200 15001570
-
(2004)
J Biol Chem
, vol.279
, Issue.19
, pp. 19800-19807
-
-
Pittler, S.1
Zhang, Y.2
Chen, S.3
Mears, A.4
Zack, D.5
Ren, Z.6
Swain, P.7
Yao, S.8
Swaroop, A.9
White, J.10
-
28
-
-
33747884762
-
In vivo function of the orphan nuclear receptor NR2E3 in establishing photoreceptor identity during mammalian retinal development
-
1592580 16868010 10.1093/hmg/ddl185
-
Cheng H Aleman T Cideciyan A Khanna R Jacobson S Swaroop A In vivo function of the orphan nuclear receptor NR2E3 in establishing photoreceptor identity during mammalian retinal development Human Molecular Genetics 2006, 15(17):2588-2602. 1592580 16868010 10.1093/hmg/ ddl185
-
(2006)
Human Molecular Genetics
, vol.15
, Issue.17
, pp. 2588-2602
-
-
Cheng, H.1
Aleman, T.2
Cideciyan, A.3
Khanna, R.4
Jacobson, S.5
Swaroop, A.6
-
29
-
-
0035733108
-
The control of the false discovery rate under dependency
-
Benjamini Y Yekutieli D The control of the false discovery rate under dependency Ann Stat 2001, 29(48):1165-1188.
-
(2001)
Ann Stat
, vol.29
, Issue.48
, pp. 1165-1188
-
-
Benjamini, Y.1
Yekutieli, D.2
-
30
-
-
18244397978
-
Gene expression in papillary thyroid carcinoma reveals highly consistent profiles
-
64980 11752453 10.1073/pnas.251547398
-
Huang Y Prasad M Lemon W Hampel H Wright F Kornacker K LiVolsi K Frankel W Kloos R Eng C Pellegata N Chapelle A Gene expression in papillary thyroid carcinoma reveals highly consistent profiles Proc Natl Acad Sci USA 2001, 98(26):15044-15049. 64980 11752453 10.1073/pnas.251547398
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.26
, pp. 15044-15049
-
-
Huang, Y.1
Prasad, M.2
Lemon, W.3
Hampel, H.4
Wright, F.5
Kornacker, K.6
LiVolsi, K.7
Frankel, W.8
Kloos, R.9
Eng, C.10
Pellegata, N.11
Chapelle, A.12
-
31
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
1239896 16199517 10.1073/pnas.0506580102
-
A S Tamayo P Mootha V Mukherjee S Ebert B Gillette M Paulovich A Pomeroy S Golub T Lander E Mesirov J Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proc Natl Acad Sci USA 2005, 102(43):15545-15550. 1239896 16199517 10.1073/pnas.0506580102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Tamayo, P.1
Mootha, V.2
Mukherjee, S.3
Ebert, B.4
Gillette, M.5
Paulovich, A.6
Pomeroy, S.7
Golub, T.8
Lander, E.9
Mesirov, J.10
-
32
-
-
44449124960
-
-
Dai M http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/ CDF_download_v8.asp
-
-
-
Dai, M.1
-
33
-
-
33846689706
-
Using GOstats to test gene lists for GO term association
-
10.1093/bioinformatics/btl567 17098774
-
Falcon S Gentleman R Using GOstats to test gene lists for GO term association Bioinformatics 2007, 23(2):257-258. 10.1093/bioinformatics/ btl567 17098774
-
(2007)
Bioinformatics
, vol.23
, Issue.2
, pp. 257-258
-
-
Falcon, S.1
Gentleman, R.2
|