-
1
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
10.1093/nar/30.1.207, 99122, 11752295
-
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210. 10.1093/nar/30.1.207, 99122, 11752295.
-
(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
-
10.1093/nar/gkg091, 165538, 12519949
-
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003, 31:68-71. 10.1093/nar/gkg091, 165538, 12519949.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 68-71
-
-
Brazma, A.1
Parkinson, H.2
Sarkans, U.3
Shojatalab, M.4
Vilo, J.5
Abeygunawardena, N.6
Holloway, E.7
Kapushesky, M.8
Kemmeren, P.9
Lara, G.G.10
Oezcimen, A.11
Rocca-Serra, P.12
Sansone, S.A.13
-
3
-
-
0141450348
-
Comparison and meta-analysis of microarray data: from the bench to the computer desk
-
10.1016/j.tig.2003.08.006, 14550631
-
Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M. Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet 2003, 19:570-577. 10.1016/j.tig.2003.08.006, 14550631.
-
(2003)
Trends Genet
, vol.19
, pp. 570-577
-
-
Moreau, Y.1
Aerts, S.2
De Moor, B.3
De Strooper, B.4
Dabrowski, M.5
-
4
-
-
53149135477
-
Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets
-
10.1371/journal.pmed.0050184, 2528050,2528050, 18767902
-
Ramasamy A, Mondry A, Holmes CC, Altman DG. Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets. PLoS Med 2008, 5:e184. 10.1371/journal.pmed.0050184, 2528050,2528050, 18767902.
-
(2008)
PLoS Med
, vol.5
-
-
Ramasamy, A.1
Mondry, A.2
Holmes, C.C.3
Altman, D.G.4
-
5
-
-
3042694117
-
Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
-
10.1073/pnas.0401994101, 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. 10.1073/pnas.0401994101, 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
-
6
-
-
0036682376
-
Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer
-
Rhodes DR, 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 Res 2002, 62:4427-4433.
-
(2002)
Cancer Res
, vol.62
, pp. 4427-4433
-
-
Rhodes, D.R.1
Barrette, T.R.2
Rubin, M.A.3
Ghosh, D.4
Chinnaiyan, A.M.5
-
7
-
-
34548127285
-
Large-scale integration of cancer microarray data identifies a robust common cancer signature
-
10.1186/1471-2105-8-275, 1950528, 17663766
-
Xu L, Geman D, Winslow RL. Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics 2007, 8:275. 10.1186/1471-2105-8-275, 1950528, 17663766.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 275
-
-
Xu, L.1
Geman, D.2
Winslow, R.L.3
-
8
-
-
49249134279
-
Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus
-
10.1186/1471-2164-9-310, 2515154, 18590522
-
Rasche A, Al-Hasani H, Herwig R. Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics 2008, 9:310. 10.1186/1471-2164-9-310, 2515154, 18590522.
-
(2008)
BMC Genomics
, vol.9
, pp. 310
-
-
Rasche, A.1
Al-Hasani, H.2
Herwig, R.3
-
9
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
-
10.1038/ng1201-365, 11726920
-
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29:365-371. 10.1038/ng1201-365, 11726920.
-
(2001)
Nat Genet
, vol.29
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
Aach, J.7
Ansorge, W.8
Ball, C.A.9
Causton, H.C.10
Gaasterland, T.11
Glenisson, P.12
Holstege, F.C.13
Kim, I.F.14
Markowitz, V.15
Matese, J.C.16
Parkinson, H.17
Robinson, A.18
Sarkans, U.19
Schulze-Kremer, S.20
Stewart, J.21
Taylor, R.22
Vilo, J.23
Vingron, M.24
more..
-
10
-
-
33750879597
-
Lack of correct data format and comparability limits future integrative microarray research
-
10.1038/nbt1106-1322, 17093466
-
Larsson O, Sandberg R. Lack of correct data format and comparability limits future integrative microarray research. Nat Biotechnol 2006, 24:1322-1323. 10.1038/nbt1106-1322, 17093466.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1322-1323
-
-
Larsson, O.1
Sandberg, R.2
-
11
-
-
58149156463
-
Statistical challenges in preprocessing in microarray experiments in cancer
-
10.1158/1078-0432.CCR-07-4532, 18829474
-
Owzar K, Barry WT, Jung SH, Sohn I, George SL. Statistical challenges in preprocessing in microarray experiments in cancer. Clin Cancer Res 2008, 14:5959-5966. 10.1158/1078-0432.CCR-07-4532, 18829474.
-
(2008)
Clin Cancer Res
, vol.14
, pp. 5959-5966
-
-
Owzar, K.1
Barry, W.T.2
Jung, S.H.3
Sohn, I.4
George, S.L.5
-
12
-
-
57049093397
-
Much room for improvement in deposition rates of expression microarray datasets
-
10.1038/nmeth1208-991, 19034265
-
Ochsner SA, Steffen DL, Stoeckert CJ, McKenna NJ. Much room for improvement in deposition rates of expression microarray datasets. Nat Methods 2008, 5:991. 10.1038/nmeth1208-991, 19034265.
-
(2008)
Nat Methods
, vol.5
, pp. 991
-
-
Ochsner, S.A.1
Steffen, D.L.2
Stoeckert, C.J.3
McKenna, N.J.4
-
13
-
-
34548499539
-
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization
-
10.1016/j.gene.2007.06.016, 2111172, 17651921
-
Cahan P, Rovegno F, Mooney D, Newman JC, St Laurent G, McCaffrey TA. Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. Gene 2007, 401:12-18. 10.1016/j.gene.2007.06.016, 2111172, 17651921.
-
(2007)
Gene
, vol.401
, pp. 12-18
-
-
Cahan, P.1
Rovegno, F.2
Mooney, D.3
Newman, J.C.4
St Laurent, G.5
McCaffrey, T.A.6
-
14
-
-
38549134505
-
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata
-
10.1093/nar/gkm815, 2238822, 17932051
-
Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, Gardner TS. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res 2008, 36:D866-870. 10.1093/nar/gkm815, 2238822, 17932051.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Faith, J.J.1
Driscoll, M.E.2
Fusaro, V.A.3
Cosgrove, E.J.4
Hayete, B.5
Juhn, F.S.6
Schneider, S.J.7
Gardner, T.S.8
-
15
-
-
27644528185
-
Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential
-
10.1186/1471-2105-6-S2-S12, 1637032, 16026597
-
Shi L, Tong W, Fang H, Scherf U, Han J, Puri RK, Frueh FW, Goodsaid FM, Guo L, Su Z, Han T, Fuscoe JC, Xu ZA, Patterson TA, Hong H, Xie Q, Perkins RG, Chen JJ, Casciano DA. Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 2005, 6(Suppl 2):S12. 10.1186/1471-2105-6-S2-S12, 1637032, 16026597.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL 2
-
-
Shi, L.1
Tong, W.2
Fang, H.3
Scherf, U.4
Han, J.5
Puri, R.K.6
Frueh, F.W.7
Goodsaid, F.M.8
Guo, L.9
Su, Z.10
Han, T.11
Fuscoe, J.C.12
Xu, Z.A.13
Patterson, T.A.14
Hong, H.15
Xie, Q.16
Perkins, R.G.17
Chen, J.J.18
Casciano, D.A.19
-
16
-
-
33847240050
-
Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions
-
10.1186/1471-2105-7-S2-S17, 1683572, 17118138
-
Han T, Melvin CD, Shi L, Branham WS, Moland CL, Pine PS, Thompson KL, Fuscoe JC. Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions. BMC Bioinformatics 2006, 7(Suppl 2):S17. 10.1186/1471-2105-7-S2-S17, 1683572, 17118138.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL 2
-
-
Han, T.1
Melvin, C.D.2
Shi, L.3
Branham, W.S.4
Moland, C.L.5
Pine, P.S.6
Thompson, K.L.7
Fuscoe, J.C.8
-
17
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
10.1038/nmeth756, 15846361
-
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W. Multiple-laboratory comparison of microarray platforms. Nat Methods 2005, 2:345-350. 10.1038/nmeth756, 15846361.
-
(2005)
Nat Methods
, vol.2
, pp. 345-350
-
-
Irizarry, R.A.1
Warren, D.2
Spencer, F.3
Kim, I.F.4
Biswal, S.5
Frank, B.C.6
Gabrielson, E.7
Garcia, J.G.8
Geoghegan, J.9
Germino, G.10
Griffin, C.11
Hilmer, S.C.12
Hoffman, E.13
Jedlicka, A.E.14
Kawasaki, E.15
Martinez-Murillo, F.16
Morsberger, L.17
Lee, H.18
Petersen, D.19
Quackenbush, J.20
Scott, A.21
Wilson, M.22
Yang, Y.23
Ye, S.Q.24
Yu, W.25
more..
-
18
-
-
39549120670
-
Celsius: a community resource for Affymetrix microarray data
-
10.1186/gb-2007-8-6-r112, 2394754, 17570842
-
Day A, Carlson MR, Dong J, O'Connor BD, Nelson SF. Celsius: a community resource for Affymetrix microarray data. Genome Biol 2007, 8:R112. 10.1186/gb-2007-8-6-r112, 2394754, 17570842.
-
(2007)
Genome Biol
, vol.8
-
-
Day, A.1
Carlson, M.R.2
Dong, J.3
O'Connor, B.D.4
Nelson, S.F.5
-
19
-
-
58149199565
-
CleanEx: new data extraction and merging tools based on MeSH term annotation
-
10.1093/nar/gkn878, 2686468, 19073704
-
Praz V, Bucher P. CleanEx: new data extraction and merging tools based on MeSH term annotation. Nucleic Acids Res 2009, 37:D880-884. 10.1093/nar/gkn878, 2686468, 19073704.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Praz, V.1
Bucher, P.2
-
20
-
-
48449092932
-
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data
-
10.1093/nar/gkn213, 2447788, 18463138
-
Ivliev AE, t Hoen PA, Villerius MP, den Dunnen JT, Brandt BW. Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. Nucleic Acids Res 2008, 36:W327-331. 10.1093/nar/gkn213, 2447788, 18463138.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Ivliev, A.E.1
t Hoen, P.A.2
Villerius, M.P.3
den Dunnen, J.T.4
Brandt, B.W.5
-
21
-
-
56649093037
-
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus
-
10.1093/bioinformatics/btn520, 2639278, 18842599
-
Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics 2008, 24:2798-2800. 10.1093/bioinformatics/btn520, 2639278, 18842599.
-
(2008)
Bioinformatics
, vol.24
, pp. 2798-2800
-
-
Zhu, Y.1
Davis, S.2
Stephens, R.3
Meltzer, P.S.4
Chen, Y.5
-
22
-
-
1642377561
-
ONCOMINE: a cancer microarray database and integrated data-mining platform
-
1635162, 15068665
-
Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 2004, 6:1-6. 1635162, 15068665.
-
(2004)
Neoplasia
, vol.6
, pp. 1-6
-
-
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
-
23
-
-
54349101605
-
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues
-
10.1186/gb-2008-9-9-r139, 2592717, 18803840
-
Kilpinen S, Autio R, Ojala K, Iljin K, Bucher E, Sara H, Pisto T, Saarela M, Skotheim RI, Bjorkman M, Mpindi JP, Haapa-Paananen S, Vainio P, Edgren H, Wolf M, Astola J, Nees M, Hautaniemi S, Kallioniemi O. Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol 2008, 9:R139. 10.1186/gb-2008-9-9-r139, 2592717, 18803840.
-
(2008)
Genome Biol
, vol.9
-
-
Kilpinen, S.1
Autio, R.2
Ojala, K.3
Iljin, K.4
Bucher, E.5
Sara, H.6
Pisto, T.7
Saarela, M.8
Skotheim, R.I.9
Bjorkman, M.10
Mpindi, J.P.11
Haapa-Paananen, S.12
Vainio, P.13
Edgren, H.14
Wolf, M.15
Astola, J.16
Nees, M.17
Hautaniemi, S.18
Kallioniemi, O.19
-
24
-
-
0036947892
-
Robust estimators for expression analysis
-
10.1093/bioinformatics/18.12.1585, 12490442
-
Hubbell E, Liu WM, Mei R. Robust estimators for expression analysis. Bioinformatics 2002, 18:1585-1592. 10.1093/bioinformatics/18.12.1585, 12490442.
-
(2002)
Bioinformatics
, vol.18
, pp. 1585-1592
-
-
Hubbell, E.1
Liu, W.M.2
Mei, R.3
-
25
-
-
0142121516
-
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
-
26
-
-
10844290766
-
A model-based background adjustment for oligonucleotide expression arrays
-
Wu ZJ, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 2004, 99:909-917.
-
(2004)
J Am Stat Assoc
, vol.99
, pp. 909-917
-
-
Wu, Z.J.1
Irizarry, R.A.2
Gentleman, R.3
Martinez-Murillo, F.4
Spencer, F.5
-
27
-
-
24644512209
-
Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis
-
10.1093/bioinformatics/bti605, 16076888
-
Wilson CL, Miller CJ. Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics 2005, 21:3683-3685. 10.1093/bioinformatics/bti605, 16076888.
-
(2005)
Bioinformatics
, vol.21
, pp. 3683-3685
-
-
Wilson, C.L.1
Miller, C.J.2
-
28
-
-
36549082873
-
MDQC: a new quality assessment method for microarrays based on quality control reports
-
10.1093/bioinformatics/btm487, 17933854
-
Cohen Freue GV, Hollander Z, Shen E, Zamar RH, Balshaw R, Scherer A, McManus B, Keown P, McMaster WR, Ng RT. MDQC: a new quality assessment method for microarrays based on quality control reports. Bioinformatics 2007, 23:3162-3169. 10.1093/bioinformatics/btm487, 17933854.
-
(2007)
Bioinformatics
, vol.23
, pp. 3162-3169
-
-
Cohen Freue, G.V.1
Hollander, Z.2
Shen, E.3
Zamar, R.H.4
Balshaw, R.5
Scherer, A.6
McManus, B.7
Keown, P.8
McMaster, W.R.9
Ng, R.T.10
-
29
-
-
58049208277
-
Power enhancement via multivariate outlier testing with gene expression arrays
-
10.1093/bioinformatics/btn591, 2638936, 19015138
-
Asare AL, Gao Z, Carey VJ, Wang R, Seyfert-Margolis V. Power enhancement via multivariate outlier testing with gene expression arrays. Bioinformatics 2009, 25:48-53. 10.1093/bioinformatics/btn591, 2638936, 19015138.
-
(2009)
Bioinformatics
, vol.25
, pp. 48-53
-
-
Asare, A.L.1
Gao, Z.2
Carey, V.J.3
Wang, R.4
Seyfert-Margolis, V.5
-
30
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
10.1186/gb-2004-5-10-r80, 545600, 15461798
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
Hornik, K.11
Hothorn, T.12
Huber, W.13
Iacus, S.14
Irizarry, R.15
Leisch, F.16
Li, C.17
Maechler, M.18
Rossini, A.J.19
Sawitzki, G.20
Smith, C.21
Smyth, G.22
Tierney, L.23
Yang, J.Y.24
Zhang, J.25
more..
-
31
-
-
65849368630
-
Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips
-
10.1093/nar/gkp168, 2677891, 19295132
-
Lee YS, Chen CH, Tsai CN, Tsai CL, Chao A, Wang TH. Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips. Nucleic Acids Res 2009, 37:e61. 10.1093/nar/gkp168, 2677891, 19295132.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Lee, Y.S.1
Chen, C.H.2
Tsai, C.N.3
Tsai, C.L.4
Chao, A.5
Wang, T.H.6
-
32
-
-
18844392338
-
Combining Affymetrix microarray results
-
10.1186/1471-2105-6-57, 1274254, 15774008
-
Stevens JR, Doerge RW. Combining Affymetrix microarray results. BMC Bioinformatics 2005, 6:57. 10.1186/1471-2105-6-57, 1274254, 15774008.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 57
-
-
Stevens, J.R.1
Doerge, R.W.2
-
33
-
-
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, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24:1151-1161. 10.1038/nbt1239, 16964229.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1151-1161
-
-
Shi, L.1
Reid, L.H.2
Jones, W.D.3
Shippy, R.4
Warrington, J.A.5
Baker, S.C.6
Collins, P.J.7
de Longueville, F.8
Kawasaki, E.S.9
Lee, K.Y.10
Luo, Y.11
Sun, Y.A.12
Willey, J.C.13
Setterquist, R.A.14
Fischer, G.M.15
Tong, W.16
Dragan, Y.P.17
Dix, D.J.18
Frueh, F.W.19
Goodsaid, F.M.20
Herman, D.21
Jensen, R.V.22
Johnson, C.D.23
Lobenhofer, E.K.24
Puri, R.K.25
Schrf, U.26
Thierry-Mieg, J.27
Wang, C.28
Wilson, M.29
Wolber, P.K.30
Zhang, L.31
Amur, S.32
Bao, W.33
Barbacioru, C.C.34
Lucas, A.B.35
Bertholet, V.36
Boysen, C.37
Bromley, B.38
Brown, D.39
Brunner, A.40
Canales, R.41
Cao, X.M.42
Cebula, T.A.43
Chen, J.J.44
Cheng, J.45
Chu, T.M.46
Chudin, E.47
Corson, J.48
Corton, J.C.49
Croner, L.J.50
Davies, C.51
Davison, T.S.52
Delenstarr, G.53
Deng, X.54
Dorris, D.55
Eklund, A.C.56
Fan, X.H.57
Fang, H.58
Fulmer-Smentek, S.59
Fuscoe, J.C.60
Gallagher, K.61
Ge, W.62
Guo, L.63
Guo, X.64
Hager, J.65
Haje, P.K.66
Han, J.67
Han, T.68
Harbottle, H.C.69
Harris, S.C.70
Hatchwell, E.71
Hauser, C.A.72
Hester, S.73
Hong, H.74
Hurban, P.75
Jackson, S.A.76
Ji, H.77
Knight, C.R.78
Kuo, W.P.79
LeClerc, J.E.80
Levy, S.81
Li, Q.Z.82
Liu, C.83
Liu, Y.84
Lombardi, M.J.85
Ma, Y.86
Magnuson, S.R.87
Maqsodi, B.88
McDaniel, T.89
Mei, N.90
Myklebost, O.91
Ning, B.92
Novoradovskaya, N.93
Orr, M.S.94
Osborn, T.W.95
Papallo, A.96
Patterson, T.A.97
Perkins, R.G.98
Peters, E.H.99
more..
-
34
-
-
47249128234
-
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses
-
10.1186/1471-2105-9-S6-S18, 2423441, 18541053
-
Stokes TH, Torrance JT, Li H, Wang MD. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. BMC Bioinformatics 2008, 9(Suppl 6):S18. 10.1186/1471-2105-9-S6-S18, 2423441, 18541053.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL 6
-
-
Stokes, T.H.1
Torrance, J.T.2
Li, H.3
Wang, M.D.4
-
35
-
-
67849128700
-
BioPortal: ontologies and integrated data resources at the click of a mouse
-
10.1093/nar/gkp440, 2703982, 19483092
-
Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 2009, 37:W170-173. 10.1093/nar/gkp440, 2703982, 19483092.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Noy, N.F.1
Shah, N.H.2
Whetzel, P.L.3
Dai, B.4
Dorf, M.5
Griffith, N.6
Jonquet, C.7
Rubin, D.L.8
Storey, M.A.9
Chute, C.G.10
Musen, M.A.11
-
36
-
-
48449086427
-
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
-
10.1093/nar/gkn252, 2447739, 18467421
-
Cote RG, Jones P, Martens L, Apweiler R, Hermjakob H. The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res 2008, 36:W372-376. 10.1093/nar/gkn252, 2447739, 18467421.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Cote, R.G.1
Jones, P.2
Martens, L.3
Apweiler, R.4
Hermjakob, H.5
-
37
-
-
23644448750
-
Genomic profiling of acquired resistance to apoptosis in cells derived from human atherosclerotic lesions: potential role of STATs, cyclinD1, BAD, and Bcl-XL
-
10.1016/j.yjmcc.2005.01.015, 16005468
-
Gagarin D, Yang Z, Butler J, Wimmer M, Du B, Cahan P, McCaffrey TA. Genomic profiling of acquired resistance to apoptosis in cells derived from human atherosclerotic lesions: potential role of STATs, cyclinD1, BAD, and Bcl-XL. J Mol Cell Cardiol 2005, 39:453-465. 10.1016/j.yjmcc.2005.01.015, 16005468.
-
(2005)
J Mol Cell Cardiol
, vol.39
, pp. 453-465
-
-
Gagarin, D.1
Yang, Z.2
Butler, J.3
Wimmer, M.4
Du, B.5
Cahan, P.6
McCaffrey, T.A.7
-
38
-
-
56649098931
-
Randomization in laboratory procedure is key to obtaining reproducible microarray results
-
10.1371/journal.pone.0003724, 2579585, 19009020
-
Yang H, Harrington CA, Vartanian K, Coldren CD, Hall R, Churchill GA. Randomization in laboratory procedure is key to obtaining reproducible microarray results. PLoS ONE 2008, 3:e3724. 10.1371/journal.pone.0003724, 2579585, 19009020.
-
(2008)
PLoS ONE
, vol.3
-
-
Yang, H.1
Harrington, C.A.2
Vartanian, K.3
Coldren, C.D.4
Hall, R.5
Churchill, G.A.6
-
39
-
-
55749111414
-
GenMiner: mining non-redundant association rules from integrated gene expression data and annotations
-
10.1093/bioinformatics/btn490, 18799482
-
Martinez R, Pasquier N, Pasquier C. GenMiner: mining non-redundant association rules from integrated gene expression data and annotations. Bioinformatics 2008, 24:2643-2644. 10.1093/bioinformatics/btn490, 18799482.
-
(2008)
Bioinformatics
, vol.24
, pp. 2643-2644
-
-
Martinez, R.1
Pasquier, N.2
Pasquier, C.3
-
40
-
-
42649134796
-
Merging two gene-expression studies via cross-platform normalization
-
10.1093/bioinformatics/btn083, 18325927
-
Shabalin AA, Tjelmeland H, Fan C, Perou CM, Nobel AB. Merging two gene-expression studies via cross-platform normalization. Bioinformatics 2008, 24:1154-1160. 10.1093/bioinformatics/btn083, 18325927.
-
(2008)
Bioinformatics
, vol.24
, pp. 1154-1160
-
-
Shabalin, A.A.1
Tjelmeland, H.2
Fan, C.3
Perou, C.M.4
Nobel, A.B.5
-
41
-
-
33845432928
-
Adjusting batch effects in microarray expression data using empirical Bayes methods
-
10.1093/biostatistics/kxj037, 16632515
-
Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8:118-127. 10.1093/biostatistics/kxj037, 16632515.
-
(2007)
Biostatistics
, vol.8
, pp. 118-127
-
-
Johnson, W.E.1
Li, C.2
Rabinovic, A.3
-
42
-
-
27844594381
-
Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
-
10.1186/1471-2105-6-265, 1312314, 16271137
-
Warnat P, Eils R, Brors B. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. BMC Bioinformatics 2005, 6:265. 10.1186/1471-2105-6-265, 1312314, 16271137.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 265
-
-
Warnat, P.1
Eils, R.2
Brors, B.3
-
43
-
-
70849131666
-
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization
-
10.1186/1471-2105-10-358, 2776026, 19863798
-
Glaab E, Garibaldi JM, Krasnogor N. ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. Bmc Bioinformatics 2009, 10:358. 10.1186/1471-2105-10-358, 2776026, 19863798.
-
(2009)
Bmc Bioinformatics
, vol.10
, pp. 358
-
-
Glaab, E.1
Garibaldi, J.M.2
Krasnogor, N.3
-
44
-
-
17744401429
-
Centralization: a new method for the normalization of gene expression data
-
Zien A, Aigner T, Zimmer R, Lengauer T. Centralization: a new method for the normalization of gene expression data. Bioinformatics 2001, 17(Suppl 1):S323-331.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL 1
-
-
Zien, A.1
Aigner, T.2
Zimmer, R.3
Lengauer, T.4
-
45
-
-
68549112747
-
A novel approach to detect differentially expressed genes from count-based digital databases by normalizing with housekeeping genes
-
10.1016/j.ygeno.2009.05.003, 19446020
-
Lu B, Yu J, Xu J, Chen J, Lai M. A novel approach to detect differentially expressed genes from count-based digital databases by normalizing with housekeeping genes. Genomics 2009, 94:211-216. 10.1016/j.ygeno.2009.05.003, 19446020.
-
(2009)
Genomics
, vol.94
, pp. 211-216
-
-
Lu, B.1
Yu, J.2
Xu, J.3
Chen, J.4
Lai, M.5
-
46
-
-
41349099850
-
Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data
-
10.1186/1471-2105-9-25, 2275243, 18199333
-
Xiong H, Zhang D, Martyniuk CJ, Trudeau VL, Xia X. Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data. BMC Bioinformatics 2008, 9:25. 10.1186/1471-2105-9-25, 2275243, 18199333.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 25
-
-
Xiong, H.1
Zhang, D.2
Martyniuk, C.J.3
Trudeau, V.L.4
Xia, X.5
-
47
-
-
0042594501
-
New normalization methods for cDNA microarray data
-
10.1093/bioinformatics/btg146, 12874043
-
Wilson DL, Buckley MJ, Helliwell CA, Wilson IW. New normalization methods for cDNA microarray data. Bioinformatics 2003, 19:1325-1332. 10.1093/bioinformatics/btg146, 12874043.
-
(2003)
Bioinformatics
, vol.19
, pp. 1325-1332
-
-
Wilson, D.L.1
Buckley, M.J.2
Helliwell, C.A.3
Wilson, I.W.4
-
48
-
-
60849113704
-
Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations
-
10.1186/1471-2105-10-S1-S24, 2648747, 19208124
-
Autio R, Kilpinen S, Saarela M, Kallioniemi O, Hautaniemi S, Astola J. Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations. BMC Bioinformatics 2009, 10(Suppl 1):S24. 10.1186/1471-2105-10-S1-S24, 2648747, 19208124.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL 1
-
-
Autio, R.1
Kilpinen, S.2
Saarela, M.3
Kallioniemi, O.4
Hautaniemi, S.5
Astola, J.6
-
49
-
-
36049000444
-
Survival prediction of stage I lung adenocarcinomas by expression of 10 genes
-
10.1172/JCI32007, 2030461, 17948124
-
Bianchi F, Nuciforo P, Vecchi M, Bernard L, Tizzoni L, Marchetti A, Buttitta F, Felicioni L, Nicassio F, Di Fiore PP. Survival prediction of stage I lung adenocarcinomas by expression of 10 genes. J Clin Invest 2007, 117:3436-3444. 10.1172/JCI32007, 2030461, 17948124.
-
(2007)
J Clin Invest
, vol.117
, pp. 3436-3444
-
-
Bianchi, F.1
Nuciforo, P.2
Vecchi, M.3
Bernard, L.4
Tizzoni, L.5
Marchetti, A.6
Buttitta, F.7
Felicioni, L.8
Nicassio, F.9
Di Fiore, P.P.10
-
50
-
-
51349088017
-
Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes
-
10.1158/1078-0432.CCR-07-4756, 18698033
-
Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, Delorenzi M, Piccart M, Sotiriou C. Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res 2008, 14:5158-5165. 10.1158/1078-0432.CCR-07-4756, 18698033.
-
(2008)
Clin Cancer Res
, vol.14
, pp. 5158-5165
-
-
Desmedt, C.1
Haibe-Kains, B.2
Wirapati, P.3
Buyse, M.4
Larsimont, D.5
Bontempi, G.6
Delorenzi, M.7
Piccart, M.8
Sotiriou, C.9
-
51
-
-
33750943691
-
Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers
-
10.1200/JCO.2006.06.7330, 17075124
-
Griffith OL, Melck A, Jones SJM, Wiseman SM. Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers. J Clin Oncol 2006, 24:5043-5051. 10.1200/JCO.2006.06.7330, 17075124.
-
(2006)
J Clin Oncol
, vol.24
, pp. 5043-5051
-
-
Griffith, O.L.1
Melck, A.2
Jones, S.J.M.3
Wiseman, S.M.4
-
52
-
-
34249807326
-
A 10-gene classifier for distinguishing head and neck squamous cell carcinoma and lung squamous cell carcinoma
-
10.1158/1078-0432.CCR-06-1670, 17504990
-
Vachani A, Nebozhyn M, Singhal S, Alila L, Wakeam E, Muschel R, Powell CA, Gaffney P, Singh B, Brose MS, Litzky LA, Kucharczuk J, Kaiser LR, Marron JS, Showe MK, Albelda SM, Showe LC. A 10-gene classifier for distinguishing head and neck squamous cell carcinoma and lung squamous cell carcinoma. Clin Cancer Res 2007, 13:2905-2915. 10.1158/1078-0432.CCR-06-1670, 17504990.
-
(2007)
Clin Cancer Res
, vol.13
, pp. 2905-2915
-
-
Vachani, A.1
Nebozhyn, M.2
Singhal, S.3
Alila, L.4
Wakeam, E.5
Muschel, R.6
Powell, C.A.7
Gaffney, P.8
Singh, B.9
Brose, M.S.10
Litzky, L.A.11
Kucharczuk, J.12
Kaiser, L.R.13
Marron, J.S.14
Showe, M.K.15
Albelda, S.M.16
Showe, L.C.17
-
53
-
-
33845877973
-
A gene expression signature predicts survival of patients with stage I non-small cell lung cancer
-
Lu Y, Lemon W, Liu PY, Yi YJ, Morrison C, Yang P, Sun ZF, Szoke J, Gerald WL, Watson M, Govindan R, You M. A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. PLos Med 2006, 3:2229-2243.
-
(2006)
PLos Med
, vol.3
, pp. 2229-2243
-
-
Lu, Y.1
Lemon, W.2
Liu, P.Y.3
Yi, Y.J.4
Morrison, C.5
Yang, P.6
Sun, Z.F.7
Szoke, J.8
Gerald, W.L.9
Watson, M.10
Govindan, R.11
You, M.12
-
54
-
-
3242885824
-
Expression Profiler: next generation--an online platform for analysis of microarray data
-
10.1093/nar/gkh470, 441608, 15215431
-
Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Korner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A. Expression Profiler: next generation--an online platform for analysis of microarray data. Nucleic Acids Res 2004, 32:W465-470. 10.1093/nar/gkh470, 441608, 15215431.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Kapushesky, M.1
Kemmeren, P.2
Culhane, A.C.3
Durinck, S.4
Ihmels, J.5
Korner, C.6
Kull, M.7
Torrente, A.8
Sarkans, U.9
Vilo, J.10
Brazma, A.11
-
55
-
-
0042121252
-
GEPAS: A web-based resource for microarray gene expression data analysis
-
10.1093/nar/gkg591, 168997, 12824345
-
Herrero J, Al-Shahrour F, Diaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J. GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res 2003, 31:3461-3467. 10.1093/nar/gkg591, 168997, 12824345.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3461-3467
-
-
Herrero, J.1
Al-Shahrour, F.2
Diaz-Uriarte, R.3
Mateos, A.4
Vaquerizas, J.M.5
Santoyo, J.6
Dopazo, J.7
-
56
-
-
40549091953
-
EzArray: a web-based highly automated Affymetrix expression array data management and analysis system
-
10.1186/1471-2105-9-46, 2265266, 18218103
-
Zhu Y, Xu W. EzArray: a web-based highly automated Affymetrix expression array data management and analysis system. BMC Bioinformatics 2008, 9:46. 10.1186/1471-2105-9-46, 2265266, 18218103.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 46
-
-
Zhu, Y.1
Xu, W.2
-
57
-
-
69849112774
-
WebArrayDB: cross-platform microarray data analysis and public data repository
-
10.1093/bioinformatics/btp430, 19602526
-
Xia XQ, McClelland M, Porwollik S, Song W, Cong X, Wang Y. WebArrayDB: cross-platform microarray data analysis and public data repository. Bioinformatics 2009, 25:2425-2429. 10.1093/bioinformatics/btp430, 19602526.
-
(2009)
Bioinformatics
, vol.25
, pp. 2425-2429
-
-
Xia, X.Q.1
McClelland, M.2
Porwollik, S.3
Song, W.4
Cong, X.5
Wang, Y.6
-
58
-
-
33747839466
-
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis
-
10.1093/nar/gkl038, 1538903, 16845058
-
Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, Trajanoski Z. CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res 2006, 34:W498-503. 10.1093/nar/gkl038, 1538903, 16845058.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Rainer, J.1
Sanchez-Cabo, F.2
Stocker, G.3
Sturn, A.4
Trajanoski, Z.5
|