-
1
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
Edgar, R., Domrachev, M. & Lash, A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
2
-
-
0037246058
-
ArrayExpress - A public repository for microarray gene expression data at the EBI
-
Brazma, A. et al. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 68-71 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 68-71
-
-
Brazma, A.1
-
3
-
-
33645473195
-
Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells
-
Ali-Seyed, M. et al. Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells. BMC Cancer 6, 54-68 (2006).
-
(2006)
BMC Cancer
, vol.6
, pp. 54-68
-
-
Ali-Seyed, M.1
-
4
-
-
18244389201
-
Standardizing global gene expression analysis between laboratories and across platforms
-
Bammler, T. et al. Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods 2, 351-356 (2005).
-
(2005)
Nat. Methods
, vol.2
, pp. 351-356
-
-
Bammler, T.1
-
5
-
-
0038486795
-
Spotted long oligonucleotide arrays for human gene expression analysis
-
Barczak, A. et al. Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res. 13, 1775-1785 (2003).
-
(2003)
Genome Res.
, vol.13
, pp. 1775-1785
-
-
Barczak, A.1
-
6
-
-
27144486151
-
Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
-
Barnes, M., Freudenberg, J., Thompson, S., Aronow, B. & Pavlidis, P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res. 33, 5914-5923 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5914-5923
-
-
Barnes, M.1
Freudenberg, J.2
Thompson, S.3
Aronow, B.4
Pavlidis, P.5
-
7
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
Irizarry, R.A. et al. Multiple-laboratory comparison of microarray platforms. Nat. Methods 2, 345-350 (2005).
-
(2005)
Nat. Methods
, vol.2
, pp. 345-350
-
-
Irizarry, R.A.1
-
8
-
-
0002922661
-
Microarray results: How accurate are they?
-
Kothapalli, R., Yoder, S.J., Mane, S. & Loughran, T.P., Jr. Microarray results: how accurate are they? BMC Bioinformatics 3, 22-32 (2002).
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 22-32
-
-
Kothapalli, R.1
Yoder, S.J.2
Mane, S.3
Loughran Jr., T.P.4
-
9
-
-
0036211063
-
Analysis of matched mRNA measurements from two different microarray technologies
-
Kuo, W.P., Jenssen, T.K., Butte, A.J., Ohno-Machado, L. & Kohane, I.S. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18, 405-412 (2002).
-
(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
-
10
-
-
18244378238
-
Independence and reproducibility across microarray platforms
-
Larkin, J.E., Frank, B.C., Gavras, H., Sultana, R. & Quackenbush, J. Independence and reproducibility across microarray platforms. Nat. Methods 2, 337-344 (2005).
-
(2005)
Nat. Methods
, vol.2
, pp. 337-344
-
-
Larkin, J.E.1
Frank, B.C.2
Gavras, H.3
Sultana, R.4
Quackenbush, J.5
-
11
-
-
1542577328
-
Comparing cDNA and oligonucleotide array data: Concordance of gene expression across platforms for the NCI-60 cancer cells
-
Lee, J.K. et al. Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biol. 4, R82-94 (2003).
-
(2003)
Genome Biol.
, vol.4
-
-
Lee, J.K.1
-
12
-
-
0036773278
-
Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays
-
Li, J., Pankratz, M. & Johnson, J.A. Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol. Sci. 69, 383-390 (2002).
-
(2002)
Toxicol. Sci.
, vol.69
, pp. 383-390
-
-
Li, J.1
Pankratz, M.2
Johnson, J.A.3
-
13
-
-
2442691827
-
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
-
Mecham, B.H. et al. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res. 32, e74-82 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Mecham, B.H.1
-
14
-
-
4143151607
-
Current issues for DNA microarrays: Platform comparison, double linear amplification, and universal RNA reference
-
Park, P.J. et al. Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J. Biotechnol. 112, 225-245 (2004).
-
(2004)
J. Biotechnol.
, vol.112
, pp. 225-245
-
-
Park, P.J.1
-
15
-
-
10744221835
-
A microarray platform comparison for neuroscience applications
-
Parrish, M.L. et al. A microarray platform comparison for neuroscience applications. J. Neurosci. Methods 132, 57-68 (2004).
-
(2004)
J. Neurosci. Methods
, vol.132
, pp. 57-68
-
-
Parrish, M.L.1
-
16
-
-
23644453736
-
Three microarray platforms: An analysis of their concordance in profiling gene expression
-
Petersen, D. et al. Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics 6, 63-77 (2005).
-
(2005)
BMC Genomics
, vol.6
, pp. 63-77
-
-
Petersen, D.1
-
17
-
-
24744458340
-
Comparison of transcript profiling on Arabidopsis microarray platform technologies
-
Pylatuik, J.D. & Fobert, P.R. Comparison of transcript profiling on Arabidopsis microarray platform technologies. Plant Mol. Biol. 58, 609-624 (2005).
-
(2005)
Plant Mol. Biol.
, vol.58
, pp. 609-624
-
-
Pylatuik, J.D.1
Fobert, P.R.2
-
18
-
-
0346670079
-
Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epithelium cell lines
-
Rogojina, A.T., Orr, W.E., Song, B.K. & Geisert, E.E., Jr. Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epithelium cell lines. Mol. Vis. 9, 482-496 (2003).
-
(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
-
19
-
-
27144529544
-
Patient-based cross-platform comparison of oligonucleotide microarray expression profiles
-
Schlingemann, J. et al. Patient-based cross-platform comparison of oligonucleotide microarray expression profiles. Lab. Invest. 85, 1024-1039 (2005).
-
(2005)
Lab. Invest.
, vol.85
, pp. 1024-1039
-
-
Schlingemann, J.1
-
20
-
-
27644528185
-
Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential
-
Shi, L. et al. Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 6 suppl. Suppl. 2, S12-S26 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.2 SUPPL.
-
-
Shi, L.1
-
21
-
-
0141905890
-
Evaluation of gene expression measurements from commercial microarray platforms
-
Tan, P.K. et al. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31, 5676-5684 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5676-5684
-
-
Tan, P.K.1
-
22
-
-
9144256854
-
Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations
-
Shippy, R. et al. Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics 5, 61-76 (2004).
-
(2004)
BMC Genomics
, vol.5
, pp. 61-76
-
-
Shippy, R.1
-
23
-
-
33644778724
-
Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates
-
Walker, S.J., Wang, Y., Grant, K.A., Chan, F. & Hellmann, G.M. Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates. J. Neurosci. Methods 152, 179-189 (2005).
-
(2005)
J. Neurosci. Methods
, vol.152
, pp. 179-189
-
-
Walker, S.J.1
Wang, Y.2
Grant, K.A.3
Chan, F.4
Hellmann, G.M.5
-
24
-
-
23844483247
-
A study of inter-lab and inter-platform agreement of DNA microarray data
-
Wang, H., He, X., Band, M., Wilson, C. & Liu, L. A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics 6, 71-80 (2005).
-
(2005)
BMC Genomics
, vol.6
, pp. 71-80
-
-
Wang, H.1
He, X.2
Band, M.3
Wilson, C.4
Liu, L.5
-
25
-
-
18544410036
-
Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays
-
Wang, H.Y. et al. Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biol. 4, R5-R18 (2003).
-
(2003)
Genome Biol.
, vol.4
-
-
Wang, H.Y.1
-
26
-
-
27844594381
-
Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
-
Warnat, P., Eils, R. & Brors, B. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. BMC Bioinformatics 6, 265-280 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 265-280
-
-
Warnat, P.1
Eils, R.2
Brors, B.3
-
27
-
-
17844379157
-
A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms
-
Woo, Y. et al. A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J. Biomol. Tech. 15, 276-284 (2004).
-
(2004)
J. Biomol. Tech.
, vol.15
, pp. 276-284
-
-
Woo, Y.1
-
28
-
-
4344660619
-
Comprehensive comparison of six microarray technologies
-
Yauk, C.L., Berndt, M.L., Williams, A. & Douglas, G.R. Comprehensive comparison of six microarray technologies. Nucleic Acids Res. 32, e124-e131 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Yauk, C.L.1
Berndt, M.L.2
Williams, A.3
Douglas, G.R.4
-
29
-
-
0037095769
-
Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays
-
Yuen, T., Wurmbach, E., Pfeffer, R.L., Ebersole, B.J. & Sealfon, S.C. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res. 30, e48-e57 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
-
-
Yuen, T.1
Wurmbach, E.2
Pfeffer, R.L.3
Ebersole, B.J.4
Sealfon, S.C.5
-
30
-
-
18844363132
-
Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays
-
Zhu, B., Ping, G., Shinohara, Y., Zhang, Y. & Baba, Y. Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays. Genomics 85, 657-665 (2005).
-
(2005)
Genomics
, vol.85
, pp. 657-665
-
-
Zhu, B.1
Ping, G.2
Shinohara, Y.3
Zhang, Y.4
Baba, Y.5
-
31
-
-
18244387702
-
Of fish and chips
-
Sherlock, G. Of fish and chips. Nat. Methods 2, 329-330 (2005).
-
(2005)
Nat. Methods
, vol.2
, pp. 329-330
-
-
Sherlock, G.1
-
32
-
-
0034730124
-
Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
-
Lee, M.L., Kuo, F.C., Whitmore, G.A. & Sklar, J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA 97, 9834-9839 (2000).
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 9834-9839
-
-
Lee, M.L.1
Kuo, F.C.2
Whitmore, G.A.3
Sklar, J.4
-
33
-
-
4844222268
-
Increased measurement accuracy for sequence-verified microarray probes
-
Mecham, B.H. et al. Increased measurement accuracy for sequence-verified microarray probes. Physiol. Genomics 18, 308-315 (2004).
-
(2004)
Physiol. Genomics
, vol.18
, pp. 308-315
-
-
Mecham, B.H.1
-
34
-
-
25444515422
-
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
-
Carter, S.L., Eklund, A.C., Mecham, B.H., Kohane, I.S. & Szallasi, Z. Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 6, 107-122 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 107-122
-
-
Carter, S.L.1
Eklund, A.C.2
Mecham, B.H.3
Kohane, I.S.4
Szallasi, Z.5
-
35
-
-
0035977135
-
Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes
-
Blackshaw, S., Fraioli, R.E., Furukawa, T. & Cepko, C.L. Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell 107, 579-589 (2001).
-
(2001)
Cell
, vol.107
, pp. 579-589
-
-
Blackshaw, S.1
Fraioli, R.E.2
Furukawa, T.3
Cepko, C.L.4
-
36
-
-
19344368188
-
Genomic analysis of mouse retinal development
-
Blackshaw, S. et al. Genomic analysis of mouse retinal development. PLoS Biol. 2, E247-E268 (2004).
-
(2004)
PLoS Biol.
, vol.2
-
-
Blackshaw, S.1
-
37
-
-
0028789793
-
Serial analysis of gene expression
-
Velculescu, V.E., Zhang, L., Vogelstein, B. & Kinzler, K.W. Serial analysis of gene expression. Science 270, 484-487 (1995).
-
(1995)
Science
, vol.270
, pp. 484-487
-
-
Velculescu, V.E.1
Zhang, L.2
Vogelstein, B.3
Kinzler, K.W.4
-
38
-
-
0034130561
-
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays
-
Brenner, S. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630-634 (2000).
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 630-634
-
-
Brenner, S.1
-
39
-
-
18844447998
-
Statistical development and evaluation of microarray gene expression data filters
-
Pounds, S. & Cheng, C. Statistical development and evaluation of microarray gene expression data filters. J. Comput. Biol. 12, 482-495 (2005).
-
(2005)
J. Comput. Biol.
, vol.12
, pp. 482-495
-
-
Pounds, S.1
Cheng, C.2
-
40
-
-
1542361725
-
Cross-site comparison of gene expression data reveals high similarity
-
Chu, T.M., Deng, S., Wolfinger, R., Paules, R.S. & Hamadeh, H.K. Cross-site comparison of gene expression data reveals high similarity. Environ. Health Perspect. 112, 449-455 (2004).
-
(2004)
Environ. Health Perspect.
, vol.112
, pp. 449-455
-
-
Chu, T.M.1
Deng, S.2
Wolfinger, R.3
Paules, R.S.4
Hamadeh, H.K.5
-
41
-
-
32144437945
-
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR
-
Qin, L.X. et al. Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. BMC Bioinformatics 7, 23 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 23
-
-
Qin, L.X.1
-
42
-
-
11144354637
-
Expression profiling using a hexamer-based universal microarray
-
Roth, M.E. et al. Expression profiling using a hexamer-based universal microarray. Nat. Biotechnol. 22, 418-426 (2004).
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 418-426
-
-
Roth, M.E.1
-
43
-
-
2442674039
-
Decoding randomly ordered DNA arrays
-
Gunderson, K.L. et al. Decoding randomly ordered DNA arrays. Genome Res. 14, 870-877 (2004).
-
(2004)
Genome Res.
, vol.14
, pp. 870-877
-
-
Gunderson, K.L.1
-
44
-
-
0037200201
-
A new non-linear normalization method for reducing variability in DNA microarray experiments
-
Workman, C. et al. A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol 3, research0048 (2002).
-
(2002)
Genome Biol.
, vol.3
-
-
Workman, C.1
-
45
-
-
13244289933
-
Optimized LOWESS normalization parameter selection for DNA microarray data
-
Berger, J.A. et al. Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinformatics 5, 194-207 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 194-207
-
-
Berger, J.A.1
-
46
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
47
-
-
0037499970
-
MatchMiner: A tool for batch navigation among gene and gene product identifiers
-
Bussey, K.J. et al. MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol. 4, R27-34 (2003).
-
(2003)
Genome Biol.
, vol.4
-
-
Bussey, K.J.1
-
48
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent, W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
49
-
-
0037208157
-
NetAffx: Affymetrix probesets and annotations
-
Liu, G. et al. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 31, 82-86 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 82-86
-
-
Liu, G.1
-
50
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman, R.C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80-R96 (2004).
-
(2004)
Genome Biol.
, vol.5
-
-
Gentleman, R.C.1
|