-
1
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher V G, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA, 2001, 98: 5116-5121.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
2
-
-
33747344944
-
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
-
Jeffery I B, Higgins D G, Culhane A C. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics, 2006, 7: 359.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 359
-
-
Jeffery, I.B.1
Higgins, D.G.2
Culhane, A.C.3
-
3
-
-
33947321935
-
Selection of differentially expressed genes in microarray data analysis
-
Chen J J, Wang S J, Tsai C A, et al. Selection of differentially expressed genes in microarray data analysis. Pharmacogenomics J, 2006.
-
(2006)
Pharmacogenomics J
-
-
Chen, J.J.1
Wang, S.J.2
Tsai, C.A.3
-
4
-
-
0037276175
-
Statistical tests for differential expression in cDNA microarray experiments
-
Cui X, Churchill G A. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol, 2003, 4: 210.
-
(2003)
Genome Biol
, vol.4
, pp. 210
-
-
Cui, X.1
Churchill, G.A.2
-
5
-
-
0141626917
-
The effect of replication on gene expression microarray experiments
-
Pavlidis P, Li Q, Noble W S. The effect of replication on gene expression microarray experiments. Bioinformatics, 2003, 19: 1620-1627.
-
(2003)
Bioinformatics
, vol.19
, pp. 1620-1627
-
-
Pavlidis, P.1
Li, Q.2
Noble, W.S.3
-
6
-
-
51749123784
-
Apparently low reproducibility of true differential expression discoveries in microarray studies
-
Zhang M, Yao C, Guo Z, et al. Apparently low reproducibility of true differential expression discoveries in microarray studies. Bioinformatics, 2008, 24: 2057-2063.
-
(2008)
Bioinformatics
, vol.24
, pp. 2057-2063
-
-
Zhang, M.1
Yao, C.2
Guo, Z.3
-
7
-
-
33748495591
-
Rat toxicogenomic study reveals analytical consistency across microarray platforms
-
Guo L, Lobenhofer E K, Wang C, et al. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol, 2006, 24: 1162-1169.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1162-1169
-
-
Guo, L.1
Lobenhofer, E.K.2
Wang, C.3
-
8
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
Shi L, Reid L H, Jones W D, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol, 2006, 24: 1151-1161.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1151-1161
-
-
Shi, L.1
Reid, L.H.2
Jones, W.D.3
-
9
-
-
29244448340
-
Microarray data analysis: from disarray to consolidation and consensus
-
Allison D B, Cui X, Page G P, et al. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet, 2006, 7: 55-65.
-
(2006)
Nat Rev Genet
, vol.7
, pp. 55-65
-
-
Allison, D.B.1
Cui, X.2
Page, G.P.3
-
10
-
-
25444476441
-
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
-
Wolfe C J, Kohane I S, Butte A J. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics, 2005, 6: 227.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 227
-
-
Wolfe, C.J.1
Kohane, I.S.2
Butte, A.J.3
-
11
-
-
4344571581
-
Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
-
Breitling R, Armengaud P, Amtmann A, et al. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett, 2004, 573: 83-92.
-
(2004)
FEBS Lett
, vol.573
, pp. 83-92
-
-
Breitling, R.1
Armengaud, P.2
Amtmann, A.3
-
12
-
-
38349188469
-
Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories
-
Yang D, Li Y, Xiao H, et al. Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories. Bioinformatics, 2008, 24: 265-271.
-
(2008)
Bioinformatics
, vol.24
, pp. 265-271
-
-
Yang, D.1
Li, Y.2
Xiao, H.3
-
13
-
-
13144305047
-
Systems biology for cancer
-
Khalil I G, Hill C. Systems biology for cancer. Curr Opin Oncol, 2005, 17: 44-48.
-
(2005)
Curr Opin Oncol
, vol.17
, pp. 44-48
-
-
Khalil, I.G.1
Hill, C.2
-
14
-
-
4043128071
-
Genetic analysis of genome-wide variation in human gene expression
-
Morley M, Molony C M, Weber T M, et al. Genetic analysis of genome-wide variation in human gene expression. Nature, 2004, 430: 743-747.
-
(2004)
Nature
, vol.430
, pp. 743-747
-
-
Morley, M.1
Molony, C.M.2
Weber, T.M.3
-
15
-
-
25444456388
-
Towards precise classification of cancers based on robust gene functional expression profiles
-
Guo Z, Zhang T, Li X, et al. Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics, 2005, 6: 58.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 58
-
-
Guo, Z.1
Zhang, T.2
Li, X.3
-
16
-
-
33846064113
-
NCBI GEO: mining tens of millions of expression profiles-database and tools update
-
Barrett T, Troup D B, Wilhite S E, et al. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res, 2007, 35: 760-765.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 760-765
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
-
17
-
-
0035923583
-
Diversity of gene expression in adenocarcinoma of the lung
-
Garber M E, Troyanskaya O G, Schluens K, et al. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA, 2001, 98: 13784-13789.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 13784-13789
-
-
Garber, M.E.1
Troyanskaya, O.G.2
Schluens, K.3
-
18
-
-
0035923521
-
Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses
-
Bhattacharjee A, Richards W G, Staunton J, et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA, 2001, 98: 13790-13795.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 13790-13795
-
-
Bhattacharjee, A.1
Richards, W.G.2
Staunton, J.3
-
19
-
-
50249185512
-
Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature
-
Galamb O, Gyorffy B, Sipos F, et al. Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature. Dis Markers, 2008, 25: 1-16.
-
(2008)
Dis Markers
, vol.25
, pp. 1-16
-
-
Galamb, O.1
Gyorffy, B.2
Sipos, F.3
-
20
-
-
37849013557
-
Transcriptome profile of human colorectal adenomas
-
Sabates-Bellver J, van der Flier L G, de Palo M, et al. Transcriptome profile of human colorectal adenomas. Mol Cancer Res, 2007, 5: 1263-1275.
-
(2007)
Mol Cancer Res
, vol.5
, pp. 1263-1275
-
-
Sabates-Bellver, J.1
van der Flier, L.G.2
de Palo, M.3
-
21
-
-
9144251970
-
Gene expression profiling identifies clinically relevant subtypes of prostate cancer
-
Lapointe J, Li C, Higgins J P, et al. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci USA, 2004, 101: 811-816.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 811-816
-
-
Lapointe, J.1
Li, C.2
Higgins, J.P.3
-
22
-
-
12444313589
-
Variation in gene expression patterns in human gastric cancers
-
Chen X, Leung S Y, Yuen S T, et al. Variation in gene expression patterns in human gastric cancers. Mol Biol Cell, 2003, 14: 3208-3215.
-
(2003)
Mol Biol Cell
, vol.14
, pp. 3208-3215
-
-
Chen, X.1
Leung, S.Y.2
Yuen, S.T.3
-
23
-
-
4744347276
-
Novel endothelial cell markers in hepatocellular carcinoma
-
Chen X, Higgins J, Cheung S T, et al. Novel endothelial cell markers in hepatocellular carcinoma. Mod Pathol, 2004, 17: 1198-1210.
-
(2004)
Mod Pathol
, vol.17
, pp. 1198-1210
-
-
Chen, X.1
Higgins, J.2
Cheung, S.T.3
-
24
-
-
20044396570
-
Integrative analysis of the cancer transcriptome
-
Rhodes D R, Chinnaiyan A M. Integrative analysis of the cancer transcriptome. Nat Genet, 2005, 37: 31-37.
-
(2005)
Nat Genet
, vol.37
, pp. 31-37
-
-
Rhodes, D.R.1
Chinnaiyan, A.M.2
-
25
-
-
0037251963
-
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
-
Diehn M, Sherlock G, Binkley G, et al. SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res, 2003, 31: 219-223.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 219-223
-
-
Diehn, M.1
Sherlock, G.2
Binkley, G.3
-
26
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball C A, Blake J A, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 2000, 25: 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
27
-
-
0036489046
-
Comparison of discrimination methods for the classification of tumours using gene expression data
-
Dudoit S, Fridlyand J, Speed T. Comparison of discrimination methods for the classification of tumours using gene expression data. J Am Statisti Associ, 2002, 97: 77-87.
-
(2002)
J Am Statisti Associ
, vol.97
, pp. 77-87
-
-
Dudoit, S.1
Fridlyand, J.2
Speed, T.3
-
28
-
-
0037388166
-
Cell and tumor classification using gene expression data: construction of forests
-
Zhang H, Yu C Y, Singer B. Cell and tumor classification using gene expression data: construction of forests. Proc Natl Acad Sci USA, 2003, 100: 4168-4172.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 4168-4172
-
-
Zhang, H.1
Yu, C.Y.2
Singer, B.3
-
29
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-
Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics, 2006, 22: 1600-1607.
-
(2006)
Bioinformatics
, vol.22
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenfuhrer, J.2
Lengauer, T.3
-
30
-
-
33846689706
-
Using GOstats to test gene lists for GO term association
-
Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics, 2007, 23: 257-258.
-
(2007)
Bioinformatics
, vol.23
, pp. 257-258
-
-
Falcon, S.1
Gentleman, R.2
-
31
-
-
0034614637
-
The hallmarks of cancer
-
Hanahan D, Weinberg R A. The hallmarks of cancer. Cell, 2000, 100: 57-70.
-
(2000)
Cell
, vol.100
, pp. 57-70
-
-
Hanahan, D.1
Weinberg, R.A.2
-
32
-
-
33749051213
-
Can NF-kappaB be a target for novel and efficient anti-cancer agents?
-
Olivier S, Robe P, Bours V. Can NF-kappaB be a target for novel and efficient anti-cancer agents? Biochem Pharmacol, 2006, 72: 1054-1068.
-
(2006)
Biochem Pharmacol
, vol.72
, pp. 1054-1068
-
-
Olivier, S.1
Robe, P.2
Bours, V.3
-
33
-
-
55449118908
-
Nuclear factor kappa B: a marker of chemotherapy for human stage IV gastric carcinoma
-
Long Y M, Ye S, Rong J, et al. Nuclear factor kappa B: a marker of chemotherapy for human stage IV gastric carcinoma. World J Gastroenterol, 2008, 14: 4739-4744.
-
(2008)
World J Gastroenterol
, vol.14
, pp. 4739-4744
-
-
Long, Y.M.1
Ye, S.2
Rong, J.3
-
34
-
-
0028568315
-
Cell cycle control and cancer
-
Hartwell L H, Kastan M B. Cell cycle control and cancer. Science, 1994, 266: 1821-1828.
-
(1994)
Science
, vol.266
, pp. 1821-1828
-
-
Hartwell, L.H.1
Kastan, M.B.2
-
35
-
-
0028556251
-
Migration-associated volume changes in neutrophils facilitate the migratory process in vitro
-
Rosengren S, Henson P M, Worthen G S. Migration-associated volume changes in neutrophils facilitate the migratory process in vitro. Am J Physiol, 1994, 267: 1623-1632.
-
(1994)
Am J Physiol
, vol.267
, pp. 1623-1632
-
-
Rosengren, S.1
Henson, P.M.2
Worthen, G.S.3
-
36
-
-
30544447053
-
Involvement of aquaporin-4 in astroglial cell migration and glial scar formation
-
Saadoun S, Papadopoulos M C, Watanabe H, et al. Involvement of aquaporin-4 in astroglial cell migration and glial scar formation. J Cell Sci, 2005, 118: 5691-5698.
-
(2005)
J Cell Sci
, vol.118
, pp. 5691-5698
-
-
Saadoun, S.1
Papadopoulos, M.C.2
Watanabe, H.3
-
37
-
-
27844461512
-
Epithelial-mesenchymal transition in development and cancer: role of phosphatidylinositol 3′ kinase/AKT pathways
-
Larue L, Bellacosa A. Epithelial-mesenchymal transition in development and cancer: role of phosphatidylinositol 3′ kinase/AKT pathways. Oncogene, 2005, 24: 7443-7454.
-
(2005)
Oncogene
, vol.24
, pp. 7443-7454
-
-
Larue, L.1
Bellacosa, A.2
-
38
-
-
56749176437
-
Cadherins and cancer: how does cadherin dysfunction promote tumor progression?
-
Jeanes A, Gottardi C J, Yap A S. Cadherins and cancer: how does cadherin dysfunction promote tumor progression? Oncogene, 2008, 27: 6920-6929.
-
(2008)
Oncogene
, vol.27
, pp. 6920-6929
-
-
Jeanes, A.1
Gottardi, C.J.2
Yap, A.S.3
-
39
-
-
0037708932
-
Metastatic potential: generic predisposition of the primary tumor or rare, metastatic variants-or both?
-
Hynes R O. Metastatic potential: generic predisposition of the primary tumor or rare, metastatic variants-or both? Cell, 2003, 113: 821-823.
-
(2003)
Cell
, vol.113
, pp. 821-823
-
-
Hynes, R.O.1
-
40
-
-
0042967678
-
BMP-2 mediates retinoid-induced apoptosis in medulloblastoma cells through a paracrine effect
-
Hallahan A R, Pritchard J I, Chandraratna R A, et al. BMP-2 mediates retinoid-induced apoptosis in medulloblastoma cells through a paracrine effect. Nat Med, 2003, 9: 1033-1038.
-
(2003)
Nat Med
, vol.9
, pp. 1033-1038
-
-
Hallahan, A.R.1
Pritchard, J.I.2
Chandraratna, R.A.3
-
41
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang H Y, Lee E, Liu Y T, et al. Network-based classification of breast cancer metastasis. Mol Syst Biol, 2007, 3: 140.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
-
42
-
-
59849125136
-
Dynamic modularity in protein interaction networks predicts breast cancer outcome
-
Taylor I W, Linding R, Warde-Farley D, et al. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol, 2009, 27: 199-204.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 199-204
-
-
Taylor, I.W.1
Linding, R.2
Warde-Farley, D.3
-
43
-
-
67649205714
-
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes
-
Zhang M, Zhang L, Zou J, et al. Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes. Bioinformatics, 2009, 25: 1662-1668.
-
(2009)
Bioinformatics
, vol.25
, pp. 1662-1668
-
-
Zhang, M.1
Zhang, L.2
Zou, J.3
-
44
-
-
6944244084
-
A module map showing conditional activity of expression modules in cancer
-
Segal E, Friedman N, Koller D, et al. A module map showing conditional activity of expression modules in cancer. Nat Genet, 2004, 36: 1090-1098.
-
(2004)
Nat Genet
, vol.36
, pp. 1090-1098
-
-
Segal, E.1
Friedman, N.2
Koller, D.3
-
45
-
-
33750937598
-
Mining expressed sequence tags identifies cancer markers of clinical interest
-
Campagne F, Skrabanek L. Mining expressed sequence tags identifies cancer markers of clinical interest. BMC Bioinformatics, 2006, 7: 481.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 481
-
-
Campagne, F.1
Skrabanek, L.2
|