-
1
-
-
0032919364
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
10.1093/nar/27.1.29, 148090, 9847135
-
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27:29-34. 10.1093/nar/27.1.29, 148090, 9847135.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
2
-
-
0034069495
-
Gene Ontology: tool for the unification of biology
-
10.1038/75556, 3037419, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
3
-
-
63449107173
-
A general modular framework for gene set enrichment analysis
-
Ackermann M, Strimmer K. A general modular framework for gene set enrichment analysis. BMC Bioinformatics 2009, 88:365-411.
-
(2009)
BMC Bioinformatics
, vol.88
, pp. 365-411
-
-
Ackermann, M.1
Strimmer, K.2
-
4
-
-
0038054341
-
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
-
10.1038/ng1180, 12808457
-
Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 2003, 34:267-273. 10.1038/ng1180, 12808457.
-
(2003)
Nat Genet
, vol.34
, pp. 267-273
-
-
Mootha, V.K.1
Lindgren, C.M.2
Eriksson, K.F.3
Subramanian, A.4
Sihag, S.5
Lehar, J.6
Puigserver, P.7
Carlsson, E.8
Ridderstrale, M.9
Laurila, E.10
Houstis, N.11
Daly, M.J.12
Patterson, N.13
Mesirov, J.P.14
Golub, T.R.15
Tamayo, P.16
Spiegelman, B.17
Lander, E.S.18
Hirschhorn, J.N.19
Altshuler, D.20
Groop, L.C.21
more..
-
5
-
-
0345832338
-
A global test for groups of genes: testing association with a clinical outcome
-
10.1093/bioinformatics/btg382, 14693814
-
Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004, 20:93-99. 10.1093/bioinformatics/btg382, 14693814.
-
(2004)
Bioinformatics
, vol.20
, pp. 93-99
-
-
Goeman, J.J.1
van de Geer, S.A.2
de Kort, F.3
van Houwelingen, H.C.4
-
6
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
10.1073/pnas.0506580102, 1239896, 16199517
-
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 USA 2005, 102:15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, 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
-
8
-
-
22944444171
-
Testing differential gene expression in functional groups. Goeman's global test versus an ANCOVA approach
-
Mansmann U, Meister R. Testing differential gene expression in functional groups. Goeman's global test versus an ANCOVA approach. Methods of Inf Med 2005, 44:449-453.
-
(2005)
Methods of Inf Med
, vol.44
, pp. 449-453
-
-
Mansmann, U.1
Meister, R.2
-
9
-
-
18744389489
-
Significance analysis of functional categories in gene expression studies: a structured permutation approach
-
10.1093/bioinformatics/bti260, 15647293
-
Barry WT, Nobel AB, Wright F. Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 2005, 21:1943-1949. 10.1093/bioinformatics/bti260, 15647293.
-
(2005)
Bioinformatics
, vol.21
, pp. 1943-1949
-
-
Barry, W.T.1
Nobel, A.B.2
Wright, F.3
-
10
-
-
33750007469
-
A multivariate approach for integrating genome-wide expression data and biological knowledge
-
10.1093/bioinformatics/btl401, 2813864, 16877751
-
Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics 2006, 22:2373-2380. 10.1093/bioinformatics/btl401, 2813864, 16877751.
-
(2006)
Bioinformatics
, vol.22
, pp. 2373-2380
-
-
Kong, S.W.1
Pu, W.T.2
Park, P.J.3
-
11
-
-
38349182215
-
Identification of differentially expressed gene categories in microarray studies using non-parametric multivariate analysis
-
10.1093/bioinformatics/btm583, 18042553
-
Nettleton D, Recknor J, Reecy JM. Identification of differentially expressed gene categories in microarray studies using non-parametric multivariate analysis. Bioinformatics 2008, 24:192-201. 10.1093/bioinformatics/btm583, 18042553.
-
(2008)
Bioinformatics
, vol.24
, pp. 192-201
-
-
Nettleton, D.1
Recknor, J.2
Reecy, J.M.3
-
12
-
-
60149104156
-
A statistical framework for testing functional categories in microarray data
-
Barry WT, Nobel AB, Wright F. A statistical framework for testing functional categories in microarray data. Annals of Applied Statistics 2008, 2:286-315.
-
(2008)
Annals of Applied Statistics
, vol.2
, pp. 286-315
-
-
Barry, W.T.1
Nobel, A.B.2
Wright, F.3
-
13
-
-
63549122405
-
Multivariate analysis of variance test for gene set analysis
-
10.1093/bioinformatics/btp098, 19254923
-
Tsai C-A, Chen JJ. Multivariate analysis of variance test for gene set analysis. Bioinformatics 2009, 25:897-903. 10.1093/bioinformatics/btp098, 19254923.
-
(2009)
Bioinformatics
, vol.25
, pp. 897-903
-
-
Tsai, C.-A.1
Chen, J.J.2
-
14
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y, Hochber Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B 1995, 57:289-300.
-
(1995)
Journal of the Royal Statistical Society. Series B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochber, Y.2
-
15
-
-
70149113077
-
R: A Language and Environment for Statistical Computing
-
ISBN 3-900051-07-0, Development Core Team
-
Development Core Team R: A Language and Environment for Statistical Computing. 2009, ISBN 3-900051-07-0, Development Core Team.
-
(2009)
-
-
-
16
-
-
84888279231
-
Maanova: Tools for analyzing Micro Array experiments
-
Wu H, Yang H, Sheppard K, Churchill G, Kerr K, Cui X. maanova: Tools for analyzing Micro Array experiments. R package version 1.20.0 2010,
-
(2010)
R package version 1.20.0
-
-
Wu, H.1
Yang, H.2
Sheppard, K.3
Churchill, G.4
Kerr, K.5
Cui, X.6
-
20
-
-
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 Biology 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
-
(2004)
Genome Biology
, 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..
-
23
-
-
42349090022
-
Penalized normal likelihood and ridge regularization of correlation and covariance matrices
-
Warton DI. Penalized normal likelihood and ridge regularization of correlation and covariance matrices. Journal of the American Statistical Association 2009, 103:340-349.
-
(2009)
Journal of the American Statistical Association
, vol.103
, pp. 340-349
-
-
Warton, D.I.1
-
24
-
-
27844521293
-
A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
-
Schafer J, Strimmer K. A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statistical Applications in Genetics and Molecular Biology 2005, 4:32.
-
(2005)
Statistical Applications in Genetics and Molecular Biology
, vol.4
, pp. 32
-
-
Schafer, J.1
Strimmer, K.2
-
25
-
-
0346961488
-
A Well-conditioned estimator for large-dimensional covariance matrices
-
Ledoit O, Wolf M. A Well-conditioned estimator for large-dimensional covariance matrices. Journal of Multivariate Analysis 2004, 88:365-411.
-
(2004)
Journal of Multivariate Analysis
, vol.88
, pp. 365-411
-
-
Ledoit, O.1
Wolf, M.2
-
26
-
-
0000235653
-
Some theorems on quadratic forms applied in the study of analysis of variance problems, I. Effect of inequality of variance in the one-way classification
-
Box GEP. Some theorems on quadratic forms applied in the study of analysis of variance problems, I. Effect of inequality of variance in the one-way classification. The Annals of Mathematical Statistics 1995, 25:290-302.
-
(1995)
The Annals of Mathematical Statistics
, vol.25
, pp. 290-302
-
-
Box, G.E.P.1
-
27
-
-
67449143322
-
Asymptotic and approximate analysis of repeated measuresd esigns under heteroscedasticity
-
Josef Eul Verlag, Lohmar, Kunert J, Trenkler G
-
Brunner E. Asymptotic and approximate analysis of repeated measuresd esigns under heteroscedasticity. mathematical statistics with applications in biometrys 2001, Josef Eul Verlag, Lohmar, Kunert J, Trenkler G.
-
(2001)
mathematical statistics with applications in biometrys
-
-
Brunner, E.1
-
28
-
-
77649330805
-
A two sample test for high dimensional data with application to gene-set testing
-
Chen SX, Qin YL. A two sample test for high dimensional data with application to gene-set testing. The Annals of Statistics 2010, 38:808-835.
-
(2010)
The Annals of Statistics
, vol.38
, pp. 808-835
-
-
Chen, S.X.1
Qin, Y.L.2
-
32
-
-
8144219516
-
Gene-expression profiles predict survival of patients with lung adenocarcinoma
-
Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JM, Iannettoni MD, Orringer MB, Hanash S. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002, 25:25-29.
-
(2002)
Nat Med
, vol.25
, pp. 25-29
-
-
Beer, D.G.1
Kardia, S.L.2
Huang, C.C.3
Giordano, T.J.4
Levin, A.M.5
Misek, D.E.6
Lin, L.7
Chen, G.8
Gharib, T.G.9
Thomas, D.G.10
Lizyness, M.L.11
Kuick, R.12
Hayasaka, S.13
Taylor, J.M.14
Iannettoni, M.D.15
Orringer, M.B.16
Hanash, S.17
-
33
-
-
77049120689
-
X-changing information on X inactivation
-
10.1016/j.yexcr.2010.01.015, 20083102
-
Barakata TS, Jonkers I, Monkhorst K, Gribnau J. X-changing information on X inactivation. Exp Cell Res 2010, 316:679-687. 10.1016/j.yexcr.2010.01.015, 20083102.
-
(2010)
Exp Cell Res
, vol.316
, pp. 679-687
-
-
Barakata, T.S.1
Jonkers, I.2
Monkhorst, K.3
Gribnau, J.4
-
34
-
-
70349694418
-
Dosage compensation and gene expression on the mammalian X chromosome: one plus one does not always equal two
-
10.1007/s10577-009-9063-9, 19802704
-
Prothero KE, Stahl JM, Carrel L. Dosage compensation and gene expression on the mammalian X chromosome: one plus one does not always equal two. Chromosome Res 2009, 17:637-648. 10.1007/s10577-009-9063-9, 19802704.
-
(2009)
Chromosome Res
, vol.17
, pp. 637-648
-
-
Prothero, K.E.1
Stahl, J.M.2
Carrel, L.3
-
35
-
-
67649884786
-
Gene set enrichment analyses revealed differences in gene expression patterns between males and females
-
2757739, 19795565
-
Zhang W, Huang RS, Duan S, Dolan ME. Gene set enrichment analyses revealed differences in gene expression patterns between males and females. In Silico Biol 2009, 9:55-63. 2757739, 19795565.
-
(2009)
In Silico Biol
, vol.9
, pp. 55-63
-
-
Zhang, W.1
Huang, R.S.2
Duan, S.3
Dolan, M.E.4
-
36
-
-
70350761428
-
ACAT2 and human hepatic cholesterol metabolism: identification of important gender-related differences in nor-molipidemic, non-obese Chinese patients
-
10.1016/j.atherosclerosis.2009.04.010, 2784173, 19467657
-
Parini P, Jiang ZY, Einarsson C, Eggertsen G, Zhang SD, Rudel LL, Han TQ, Eriksson M. ACAT2 and human hepatic cholesterol metabolism: identification of important gender-related differences in nor-molipidemic, non-obese Chinese patients. Atherosclerosis 2009, 207:266-271. 10.1016/j.atherosclerosis.2009.04.010, 2784173, 19467657.
-
(2009)
Atherosclerosis
, vol.207
, pp. 266-271
-
-
Parini, P.1
Jiang, Z.Y.2
Einarsson, C.3
Eggertsen, G.4
Zhang, S.D.5
Rudel, L.L.6
Han, T.Q.7
Eriksson, M.8
-
37
-
-
70349781856
-
Loss of mitogen-activated protein kinase kinase kinase 4 (MAP3K4) reveals a requirement for MAPK signalling in mouse sex determination
-
10.1371/journal.pbio.1000196, 2733150, 19753101
-
Bogani D, Siggers P, Brixey R, Warr N, Beddow S, Edwards J, Williams D, Wilhelm D, Koopman P, Flavell RA, Chi H, Ostrer H, Wells S, Cheeseman M, Greenfield A. Loss of mitogen-activated protein kinase kinase kinase 4 (MAP3K4) reveals a requirement for MAPK signalling in mouse sex determination. PLoS Biol 2009, 7:e1000196. 10.1371/journal.pbio.1000196, 2733150, 19753101.
-
(2009)
PLoS Biol
, vol.7
-
-
Bogani, D.1
Siggers, P.2
Brixey, R.3
Warr, N.4
Beddow, S.5
Edwards, J.6
Williams, D.7
Wilhelm, D.8
Koopman, P.9
Flavell, R.A.10
Chi, H.11
Ostrer, H.12
Wells, S.13
Cheeseman, M.14
Greenfield, A.15
-
38
-
-
63849234720
-
Determination of physiological plasma pentraxin 3 (PTX3) levels in healthy populations
-
10.1515/CCLM.2009.110, 19327124
-
Yamasaki K, Kurimura M, Kasai T, Sagara M, Kodama T, Inoue K. Determination of physiological plasma pentraxin 3 (PTX3) levels in healthy populations. Clin Chem Lab Med 2009, 47:471-477. 10.1515/CCLM.2009.110, 19327124.
-
(2009)
Clin Chem Lab Med
, vol.47
, pp. 471-477
-
-
Yamasaki, K.1
Kurimura, M.2
Kasai, T.3
Sagara, M.4
Kodama, T.5
Inoue, K.6
-
39
-
-
55049096678
-
Role of sex and time of blood sampling in SOD1 and SOD2 expression variability
-
10.1016/j.clinbiochem.2008.08.064, 18775420
-
Khymenets O, Covas MI, Farre M, Langohr K, Fito M, de la Torre R. Role of sex and time of blood sampling in SOD1 and SOD2 expression variability. Clin Biochem 2008, 41:1348-1354. 10.1016/j.clinbiochem.2008.08.064, 18775420.
-
(2008)
Clin Biochem
, vol.41
, pp. 1348-1354
-
-
Khymenets, O.1
Covas, M.I.2
Farre, M.3
Langohr, K.4
Fito, M.5
de la Torre, R.6
-
40
-
-
42749084082
-
The impact of p53 and p73 on aneuploidy and cancer
-
10.1016/j.tcb.2008.03.003, 18406616
-
Tomasini R, Mark TW, Melino G. The impact of p53 and p73 on aneuploidy and cancer. Trends Cell Biol 2008, 18:244-252. 10.1016/j.tcb.2008.03.003, 18406616.
-
(2008)
Trends Cell Biol
, vol.18
, pp. 244-252
-
-
Tomasini, R.1
Mark, T.W.2
Melino, G.3
-
41
-
-
0029793416
-
Repression of interleukin-2 and interleukin- 4 promoters by tumor suppressor protein p53
-
10.1089/jir.1996.16.595, 8877730
-
Pesch J, Brehm U, Staib C, Grummt F. Repression of interleukin-2 and interleukin- 4 promoters by tumor suppressor protein p53. J Interferon Cytokine Res 1996, 16:595-600. 10.1089/jir.1996.16.595, 8877730.
-
(1996)
J Interferon Cytokine Res
, vol.16
, pp. 595-600
-
-
Pesch, J.1
Brehm, U.2
Staib, C.3
Grummt, F.4
-
42
-
-
0001080345
-
Identification of an additional p53-responsive site in the human epidermal growth factor receptor gene promotor
-
10.1038/sj.onc.1201264, 9285564
-
Sheikh MS, Carrier F, Johnson AC, Ogdon SE, Fornace AJ. Identification of an additional p53-responsive site in the human epidermal growth factor receptor gene promotor. Oncogene 1997, 15:1095-1101. 10.1038/sj.onc.1201264, 9285564.
-
(1997)
Oncogene
, vol.15
, pp. 1095-1101
-
-
Sheikh, M.S.1
Carrier, F.2
Johnson, A.C.3
Ogdon, S.E.4
Fornace, A.J.5
-
43
-
-
34347209447
-
NGF-mediated transcriptional targets of p53 in PC12 neuronal differentiation
-
10.1186/1471-2164-8-139, 1894799, 17540029
-
Brynczka C, Labhart P, Merrick BA. NGF-mediated transcriptional targets of p53 in PC12 neuronal differentiation. BMC Genomics 2007, 8:139. 10.1186/1471-2164-8-139, 1894799, 17540029.
-
(2007)
BMC Genomics
, vol.8
, pp. 139
-
-
Brynczka, C.1
Labhart, P.2
Merrick, B.A.3
-
44
-
-
34249043939
-
Negative regulation of chemokine receptor CXCR4 by tumor suppressor p53 in breast cancer cells: implications of p53 mutation or isoform expression on breast cancer cell invasion
-
10.1038/sj.onc.1210120, 17130833
-
Mehta SA, Christopherson KW, Bhat-Nakshatri P, Goulet RJ, Broxmeyer HE, Kopelovich L, Nakshatri H. Negative regulation of chemokine receptor CXCR4 by tumor suppressor p53 in breast cancer cells: implications of p53 mutation or isoform expression on breast cancer cell invasion. Oncogene 2007, 26:3329-3337. 10.1038/sj.onc.1210120, 17130833.
-
(2007)
Oncogene
, vol.26
, pp. 3329-3337
-
-
Mehta, S.A.1
Christopherson, K.W.2
Bhat-Nakshatri, P.3
Goulet, R.J.4
Broxmeyer, H.E.5
Kopelovich, L.6
Nakshatri, H.7
-
45
-
-
0034601013
-
The GTPase rho controls a p53-dependent survival check-point during thymopoiesis
-
10.1084/jem.192.1.77, 1887705, 10880528
-
Costello PS, Cleverley SC, Galandrini R, Henning SW, Cantrell DA. The GTPase rho controls a p53-dependent survival check-point during thymopoiesis. J Exp Med 2000, 192:77-85. 10.1084/jem.192.1.77, 1887705, 10880528.
-
(2000)
J Exp Med
, vol.192
, pp. 77-85
-
-
Costello, P.S.1
Cleverley, S.C.2
Galandrini, R.3
Henning, S.W.4
Cantrell, D.A.5
-
46
-
-
51649114848
-
Kinetics of repression by modified p53 on the PDGF beta-receptor promoter
-
10.1002/ijc.23735, 18697203
-
Yang W, Wetterskog D, Matsumoto Y, Funa K. Kinetics of repression by modified p53 on the PDGF beta-receptor promoter. Int J Cancer 2008, 123:2020-2030. 10.1002/ijc.23735, 18697203.
-
(2008)
Int J Cancer
, vol.123
, pp. 2020-2030
-
-
Yang, W.1
Wetterskog, D.2
Matsumoto, Y.3
Funa, K.4
|