-
1
-
-
0036902193
-
Gene expression studies using microarrays: Principles, problems, and prospects
-
12443997
-
Murphy D Gene expression studies using microarrays: Principles, problems, and prospects Adv Physiol Educ 2000, 26(1-4):256-270. 12443997
-
(2000)
Adv Physiol Educ
, vol.26
, Issue.1-4
, pp. 256-270
-
-
Murphy, D.1
-
2
-
-
34250799882
-
Perspectives and limitations of microarray-based gene expression profiling of thyroid tumors
-
10.1210/er.2006-0047 17353294
-
Eszlinger M Krohn K Kukulska A Jarzab B Paschke R Perspectives and limitations of microarray-based gene expression profiling of thyroid tumors Endocr Rev 2007, 28(3):322-338. 10.1210/er.2006-0047 17353294
-
(2007)
Endocr Rev
, vol.28
, Issue.3
, pp. 322-338
-
-
Eszlinger, M.1
Krohn, K.2
Kukulska, A.3
Jarzab, B.4
Paschke, R.5
-
3
-
-
33748912421
-
Microarray data reproduced, but some concerns remain
-
10.1126/science.313.5793.1559a 16973852
-
Couzin J Microarray data reproduced, but some concerns remain Science 2006, 313:5793-1559. 10.1126/science.313.5793.1559a 16973852
-
(2006)
Science
, vol.313
, pp. 1559
-
-
Couzin, J.1
-
4
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter- And intraplatform reproducibility of gene expression measurements
-
10.1038/nbt1239 16964229
-
Shi L Reid LH Jones WD Shippy R Warrington JA The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat Biotechnol 2006, 24(9):1151-1161. 10.1038/nbt1239 16964229
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, pp. 1151-1161
-
-
Shi, L.1
Reid, L.H.2
Jones, W.D.3
Shippy, R.4
Warrington, J.A.5
-
5
-
-
33748491718
-
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project
-
10.1038/nbt1242 16964228
-
Patterson TA Lobenhofer EK Fulmer-Smentek SB Collins PJ Chu TM Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project Nat Biotechnol 2006, 24(9):1140-1150. 10.1038/nbt1242 16964228
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, pp. 1140-1150
-
-
Patterson, T.A.1
Lobenhofer, E.K.2
Fulmer-Smentek, S.B.3
Collins, P.J.4
Chu, T.M.5
-
6
-
-
33748495591
-
Rat toxicogenomic study reveals analytical consistency across microarray platforms
-
10.1038/nbt1238 17061323
-
Guo L Lobenhofer EK Wang C Shippy R Harris SC Rat toxicogenomic study reveals analytical consistency across microarray platforms Nat Biotechnol 2006, 24(9):1162-1169. 10.1038/nbt1238 17061323
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, pp. 1162-1169
-
-
Guo, L.1
Lobenhofer, E.K.2
Wang, C.3
Shippy, R.4
Harris, S.C.5
-
7
-
-
33748503420
-
Evaluation of DNA microarray results with quantitative gene expression platforms
-
10.1038/nbt1236 16964225
-
Canales RD Luo Y Willey JC Austermiller B Barbacioru CC Evaluation of DNA microarray results with quantitative gene expression platforms Nat Biotechnol 2006, 24(9):1115-1122. 10.1038/nbt1236 16964225
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, pp. 1115-1122
-
-
Canales, R.D.1
Luo, Y.2
Willey, J.C.3
Austermiller, B.4
Barbacioru, C.C.5
-
8
-
-
33748482861
-
Using RNA sample titrations to assess microarray platform performance and normalization techniques
-
10.1038/nbt1241 16964226
-
Shippy R Fulmer-Smentek S Jensen RV Jones WD Wolber PK Using RNA sample titrations to assess microarray platform performance and normalization techniques Nat Biotechnol 2006, 24(9):1123-1131. 10.1038/nbt1241 16964226
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, pp. 1123-1131
-
-
Shippy, R.1
Fulmer-Smentek, S.2
Jensen, R.V.3
Jones, W.D.4
Wolber, P.K.5
-
9
-
-
33748508012
-
Evaluation of external RNA controls for the assessment of microarray performance
-
10.1038/nbt1239 16964227
-
Shi L Jones WD Jensen RV Wolfinger RD Kawasaki ES Evaluation of external RNA controls for the assessment of microarray performance Nat Biotechnol 2006, 24(9):1132-1139. 10.1038/nbt1239 16964227
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, pp. 1132-1139
-
-
Shi, L.1
Jones, W.D.2
Jensen, R.V.3
Wolfinger, R.D.4
Kawasaki, E.S.5
-
10
-
-
39149111585
-
Reproducible and reliable microarray results through quality control: Good laboratory proficiency and appropriate data analysis practices are essential
-
10.1016/j.copbio.2007.11.003 18155896
-
Shi L Perkins RG Fang H Tong W Reproducible and reliable microarray results through quality control: Good laboratory proficiency and appropriate data analysis practices are essential Curr Opin Biotechnol 2007, 19(1):10-18. 10.1016/j.copbio.2007.11.003 18155896
-
(2007)
Curr Opin Biotechnol
, vol.19
, Issue.1
, pp. 10-18
-
-
Shi, L.1
Perkins, R.G.2
Fang, H.3
Tong, W.4
-
11
-
-
38349088960
-
Reproducibility of microarray data: A further analysis of microarray quality control (MAQC) data
-
2204045 10.1186/1471-2105-8-412
-
Chen J Hsueh HM Delongchamp R Lin CJ Tsai CA Reproducibility of microarray data: A further analysis of microarray quality control (MAQC) data BMC Bioinformatics 2007, 8:412. 2204045 17961233 10.1186/ 1471-2105-8-412
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 412
-
-
Chen, J.1
Hsueh, H.M.2
Delongchamp, R.3
Lin, C.J.4
Tsai, C.A.5
-
13
-
-
48949111944
-
-
The Gene Ontology (GO) project http://www.geneontology.org
-
-
-
-
14
-
-
30044434256
-
The mononuclear phagocyte system
-
10.1016/j.coi.2005.11.008 16338128
-
Hume DA The mononuclear phagocyte system Curr Opin Immunol 2006, 18(1):49-53. 10.1016/j.coi.2005.11.008 16338128
-
(2006)
Curr Opin Immunol
, vol.18
, Issue.1
, pp. 49-53
-
-
Hume, D.A.1
-
15
-
-
33645729560
-
Inflammation and atherosclerosis
-
10.1146/annurev.pathol.1.110304.100100 18039117
-
Hansson GK Robertson AK Söderberg-Nauclér C Inflammation and atherosclerosis Annu Rev Pathol 2006, 1:297-329. 10.1146/ annurev.pathol.1.110304.100100 18039117
-
(2006)
Annu Rev Pathol
, vol.1
, pp. 297-329
-
-
Hansson, G.K.1
Robertson, A.K.2
Söderberg-Nauclér, C.3
-
16
-
-
10544256600
-
Expression monitoring by hybridization to high-density oligonucleotide arrays
-
10.1038/nbt1296-1675 9634850
-
Lockhart DJ Dong H Byrne MC Follettie MT Gallo MV Expression monitoring by hybridization to high-density oligonucleotide arrays Nat Biotechnol 1996, 14(13):1675-1680. 10.1038/nbt1296-1675 9634850
-
(1996)
Nat Biotechnol
, vol.14
, Issue.13
, pp. 1675-1680
-
-
Lockhart, D.J.1
Dong, H.2
Byrne, M.C.3
Follettie, M.T.4
Gallo, M.V.5
-
18
-
-
27144486151
-
Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
-
1258170 16237126 10.1093/nar/gki890
-
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 2005, 33(18):5914-5923. 1258170 16237126 10.1093/nar/gki890
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.18
, pp. 5914-5923
-
-
Barnes, M.1
Freudenberg, J.2
Thompson, S.3
Aronow, B.4
Pavlidis, P.5
-
19
-
-
33746847084
-
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes
-
1524919 10.1093/nar/gkl485
-
Le Brigand K Russell R Moreilhon C Rouillard JM Jost B An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes Nucleic Acids Res 2006, 34(12):e87. 1524919 16855282 10.1093/nar/gkl485
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.12
-
-
Le Brigand, K.1
Russell, R.2
Moreilhon, C.3
Rouillard, J.M.4
Jost, B.5
-
20
-
-
4344706372
-
Functional plasticity of macrophages: Reversible adaptation to changing microenvironments
-
1201486 10.1189/jlb.0504272
-
Stout RD Suttles J Functional plasticity of macrophages: Reversible adaptation to changing microenvironments J Leukoc Biol 2004, 76(3):509-513. 1201486 15218057 10.1189/jlb.0504272
-
(2004)
J Leukoc Biol
, vol.76
, pp. 509-513
-
-
Stout, R.D.1
Suttles, J.2
-
21
-
-
33845865804
-
cDNA microarray analysis reveals fundamental differences in the expression profiles of primary human monocytes, monocyte-derived macrophages, and alveolar macrophages
-
10.1189/jlb.0206124 17046970
-
Li J Pritchard DK Wang X Park DR Bumgarner RE cDNA microarray analysis reveals fundamental differences in the expression profiles of primary human monocytes, monocyte-derived macrophages, and alveolar macrophages J Leukoc Biol 2007, 81(1):328-335. 10.1189/jlb.0206124 17046970
-
(2007)
J Leukoc Biol
, vol.81
, Issue.1
, pp. 328-335
-
-
Li, J.1
Pritchard, D.K.2
Wang, X.3
Park, D.R.4
Bumgarner, R.E.5
-
22
-
-
33744804832
-
Comparison of the latest commercial short and long oligonucleotide microarray technologies
-
10.1186/1471-2164-7-51 16539734 1473202
-
De Reyniès A Geromin D Cayuela JM Petel F Dessen P Sigaux F Rickman DS Comparison of the latest commercial short and long oligonucleotide microarray technologies BMC Genomics 2006, 15:7-51. 10.1186/1471-2164-7-51 16539734 1473202
-
(2006)
BMC Genomics
, vol.15
, pp. 7-51
-
-
De Reyniès, A.1
Geromin, D.2
Cayuela, J.M.3
Petel, F.4
Dessen, P.5
Sigaux, F.6
Rickman, D.S.7
-
23
-
-
34250872205
-
Three methods for optimization of cross-laboratory and cross-platform microarray expression data
-
1904274 10.1093/nar/gkl1133
-
Stafford P Brun M Three methods for optimization of cross-laboratory and cross-platform microarray expression data Nucleic Acids Res 2007, 35(10):e72. 1904274 17478523 10.1093/nar/gkl1133
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.10
-
-
Stafford, P.1
Brun, M.2
-
24
-
-
33845345622
-
A rapid method for microarray cross platform comparisons using gene expression signatures
-
10.1016/j.mcp.2006.07.004 16982174
-
Cheadle C Becker KG Cho-Chung YS Nesterova M Watkins T A rapid method for microarray cross platform comparisons using gene expression signatures Mol Cell Probes 2007, 21(1):35-46. 10.1016/j.mcp.2006.07.004 16982174
-
(2007)
Mol Cell Probes
, vol.21
, pp. 35-46
-
-
Cheadle, C.1
Becker, K.G.2
Cho-Chung, Y.S.3
Nesterova, M.4
Watkins, T.5
-
25
-
-
34248532878
-
Selection of differentially expressed genes in microarray data analysis
-
10.1038/sj.tpj.6500412 16940966
-
Chen JJ Wang SJ Tsai CA Lin CJ Selection of differentially expressed genes in microarray data analysis Pharmacogenomics J 2007, 7:212-220. 10.1038/sj.tpj.6500412 16940966
-
(2007)
Pharmacogenomics J
, vol.7
, pp. 212-220
-
-
Chen, J.J.1
Wang, S.J.2
Tsai, C.A.3
Lin, C.J.4
-
26
-
-
34347342575
-
QA/QC issues to aid regulatory acceptance of microarray gene expression data
-
10.1002/em.20293 17567852
-
Fuscoe JC Tong W Shi L QA/QC issues to aid regulatory acceptance of microarray gene expression data Environ Mol Mutagen 2007, 48(5):349-353. 10.1002/em.20293 17567852
-
(2007)
Environ Mol Mutagen
, vol.48
, Issue.5
, pp. 349-353
-
-
Fuscoe, J.C.1
Tong, W.2
Shi, L.3
-
27
-
-
34249663294
-
Analyzing gene expression data in terms of gene sets: Methodological issues
-
10.1093/bioinformatics/btm051 17303618
-
Goeman JJ Bühlmann P Analyzing gene expression data in terms of gene sets: Methodological issues Bioinformatics 2007, 23(8):980-987. 10.1093/bioinformatics/btm051 17303618
-
(2007)
Bioinformatics
, vol.23
, Issue.8
, pp. 980-987
-
-
Goeman, J.J.1
Bühlmann, P.2
-
28
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
16199517 1239896
-
Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich A Pomeroy SL Golub TR Lander ES Mesirov JP Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proc Natl Acad Sci U S A 2005, 102(43):15545-15550. 16199517 10.1073/pnas.0506580102 1239896
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
29
-
-
33750813483
-
Transcriptional profiling of the human monocyte-to-macrophage differentiation and polarization: New molecules and patterns of gene expression
-
17082649
-
Martinez FO Gordon S Locati M Mantovani A Transcriptional profiling of the human monocyte-to-macrophage differentiation and polarization: New molecules and patterns of gene expression J Immunol 2006, 177:7303-7311. 17082649
-
(2006)
J Immunol
, vol.177
, pp. 7303-7311
-
-
Martinez, F.O.1
Gordon, S.2
Locati, M.3
Mantovani, A.4
-
30
-
-
0030305457
-
R: A language for data analysis and graphics
-
10.2307/1390807
-
Ihaka R Gentleman R R: A language for data analysis and graphics Journal Comput Graph Stat 1996, 5(3):299-314. 10.2307/1390807
-
(1996)
Journal Comput Graph Stat
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
31
-
-
34548578033
-
Quality control and low-level statistical analysis of Illumina BeadArrays
-
Dunning M Thorne NP Camilier I Smith ML Tavaré S Quality control and low-level statistical analysis of Illumina BeadArrays Revstat 2006, 4:1-30. http://www.ine.pt/revstat/pdf/rs060101.pdf
-
(2006)
Revstat
, vol.4
, pp. 1-30
-
-
Dunning, M.1
Thorne, N.P.2
Camilier, I.3
Smith, M.L.4
Tavaré, S.5
-
33
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
545600 10.1186/gb-2004-5-10-r80
-
Gentleman RC Carey VJ Bates DM Bolstad B Dettling M Bioconductor: Open software development for computational biology and bioinformatics Genome Biol 2004, 5:R80. 545600 15461798 10.1186/gb-2004-5-10-r80
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
-
34
-
-
0242333835
-
Normalization of cDNA microarray data
-
14597310 10.1016/S1046-2023(03)00155-5
-
Smyth GK Speed TP Normalization of cDNA microarray data Methods 2003, 31:265-273. 14597310 10.1016/S1046-2023(03)00155-5
-
(2003)
Methods
, vol.31
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.P.2
-
35
-
-
0037208157
-
NetAffx: Affymetrix probesets and annotations
-
165568 10.1093/nar/gkg121
-
Liu G Loraine AE Shigeta R Cline M Cheng J NetAffx: Affymetrix probesets and annotations Nucleic Acids Res 2003, 31(1):82-86. 165568 12519953 10.1093/nar/gkg121
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 82-86
-
-
Liu, G.1
Loraine, A.E.2
Shigeta, R.3
Cline, M.4
Cheng, J.5
-
36
-
-
34447307934
-
Mediante: A web-based microarray data manager
-
10.1093/bioinformatics/btm106 17384016
-
Le Brigand K Barbry P Mediante: A web-based microarray data manager Bioinformatics 2007, 23(10):1304-1306. 10.1093/bioinformatics/btm106 17384016
-
(2007)
Bioinformatics
, vol.23
, Issue.10
, pp. 1304-1306
-
-
Le Brigand, K.1
Barbry, P.2
-
38
-
-
48949111943
-
-
Illumina http://www.switchtoi.com
-
Illumina
-
-
-
39
-
-
48949111941
-
-
NCBI reference sequences (RefSeq) http://www.ncbi.nlm.nih.gov/RefSeq/
-
-
-
-
41
-
-
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 R Stat Soc B 1995, 57(1):289-300. http://www.jstor.org/pss/2346101
-
(1995)
J R Stat Soc B
, vol.57
, Issue.1
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
42
-
-
0036020892
-
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(3):479-498. http://www.ingentaconnect.com/content/bpl/rssb/2002/ 00000064/00000003/art00346 10.1111/1467-9868.00346
-
(2002)
J R Stat Soc B
, vol.64
, Issue.3
, pp. 479-498
-
-
Storey, J.D.1
-
43
-
-
15844417905
-
Simple procedure for estimating the false discovery rate
-
10.1093/bioinformatics/bti063 15479710
-
Dalmasso C Broet P Moreau TA Simple procedure for estimating the false discovery rate Bioinformatics 2005, 21(5):660-668. 10.1093/ bioinformatics/bti063 15479710
-
(2005)
Bioinformatics
, vol.21
, Issue.5
, pp. 660-668
-
-
Dalmasso, C.1
Broet, P.2
Moreau, T.A.3
-
44
-
-
48949111933
-
-
Panther Classification System http://www.pantherdb.org
-
-
-
-
45
-
-
0034283844
-
Transcription, genomes, function
-
10.1016/S0168-9525(00)02065-5 10973070
-
Chao RJ Cambpell MJ Transcription, genomes, function Trends in Genetics 2000, 16(9):409-415. 10.1016/S0168-9525(00)02065-5 10973070
-
(2000)
Trends in Genetics
, vol.16
, pp. 409-415
-
-
Chao, R.J.1
Cambpell, M.J.2
|