-
1
-
-
26444608611
-
Discovering statistically significant pathways in expression profiling studies
-
Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proceedings of the National Academy of Sciences 2005, 102(38):13544-13549.
-
(2005)
Proceedings of the National Academy of Sciences
, vol.102
, Issue.38
, pp. 13544-13549
-
-
Tian, L.1
Greenberg, S.A.2
Kong, S.W.3
Altschuler, J.4
Kohane, I.S.5
Park, P.J.6
-
2
-
-
25444502609
-
PAGE: parametric analysis of gene set enrichment
-
10.1186/1471-2105-6-144, 1183189, 15941488
-
Kim SY, Volsky DJ. PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 2005, 6:144. 10.1186/1471-2105-6-144, 1183189, 15941488.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 144
-
-
Kim, S.Y.1
Volsky, D.J.2
-
3
-
-
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. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 2003, 34(3):267-273. 10.1038/ng1180, 12808457.
-
(2003)
Nat Genet
, vol.34
, Issue.3
, 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
-
4
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
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. Proceedings of the National Academy of Sciences 2005, 102(43):15545-15550.
-
(2005)
Proceedings of the National Academy of Sciences
, 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
-
5
-
-
24644470505
-
Ontological analysis of gene expression data: current tools, limitations, and open problems
-
10.1093/bioinformatics/bti565, 2435250, 15994189
-
Khatri P, Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21(18):3587-3595. 10.1093/bioinformatics/bti565, 2435250, 15994189.
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3587-3595
-
-
Khatri, P.1
Draghici, S.2
-
6
-
-
34249663294
-
Analyzing gene expression data in terms of gene sets: methodological issues
-
10.1093/bioinformatics/btm051, 17303618
-
Goeman JJ, Buhlmann 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
Buhlmann, P.2
-
7
-
-
33750007469
-
A multivariate approach for integrating genome-wide expression data and biological knowledge
-
10.1093/bioinformatics/btl401, 16877751
-
Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics 2006, 22(19):2373-2380. 10.1093/bioinformatics/btl401, 16877751.
-
(2006)
Bioinformatics
, vol.22
, Issue.19
, pp. 2373-2380
-
-
Kong, S.W.1
Pu, W.T.2
Park, P.J.3
-
8
-
-
58049141153
-
Microarray-based gene set analysis: a comparison of current methods
-
10.1186/1471-2105-9-502, 2607289, 19038052
-
Song S, Black MA. Microarray-based gene set analysis: a comparison of current methods. BMC Bioinformatics 2008, 9:502. 10.1186/1471-2105-9-502, 2607289, 19038052.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 502
-
-
Song, S.1
Black, M.A.2
-
13
-
-
36549072440
-
Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data
-
10.1093/bioinformatics/btm488, 17933851
-
Tai F, Pan W. Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data. Bioinformatics 2007, 23(23):3170-3177. 10.1093/bioinformatics/btm488, 17933851.
-
(2007)
Bioinformatics
, vol.23
, Issue.23
, pp. 3170-3177
-
-
Tai, F.1
Pan, W.2
-
14
-
-
70449374222
-
Penalized model-based clustering with cluster-specific diagonal covariance matrices and grouped variables
-
Xie B, Pan W, Shen X. Penalized model-based clustering with cluster-specific diagonal covariance matrices and grouped variables. Electronic Journal of Statistics 2008, 2:168-212.
-
(2008)
Electronic Journal of Statistics
, vol.2
, pp. 168-212
-
-
Xie, B.1
Pan, W.2
Shen, X.3
-
18
-
-
27844521293
-
A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
-
Schäfer 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(1):32.
-
(2005)
Statistical Applications in Genetics and Molecular Biology
, vol.4
, Issue.1
, pp. 32
-
-
Schäfer, J.1
Strimmer, K.2
-
19
-
-
18844398070
-
Permutation Methods: A Basis for Exact Inference
-
Ernst MD. Permutation Methods: A Basis for Exact Inference. Statistical Science 2004, 19(4):676-685.
-
(2004)
Statistical Science
, vol.19
, Issue.4
, pp. 676-685
-
-
Ernst, M.D.1
-
21
-
-
84870486790
-
The Comprehensive R Archive Network
-
The Comprehensive R Archive Network. , http://cran.r-project.org
-
-
-
-
22
-
-
25144474547
-
Hotelling's T 2 multivariate profiling for detecting differential expression in microarrays
-
10.1093/bioinformatics/bti496, 15905280
-
Lu Y, Liu PY, Xiao P, Deng HW. Hotelling's T 2 multivariate profiling for detecting differential expression in microarrays. Bioinformatics 2005, 21(14):3105-3113. 10.1093/bioinformatics/bti496, 15905280.
-
(2005)
Bioinformatics
, vol.21
, Issue.14
, pp. 3105-3113
-
-
Lu, Y.1
Liu, P.Y.2
Xiao, P.3
Deng, H.W.4
-
23
-
-
2942677611
-
Multivariate exploratory tools for microarray data analysis
-
10.1093/biostatistics/4.4.555, 14557111
-
Szabo A, Boucher K, Jones D, Tsodikov AD, Klebanov LEVB, Yakovlev AY. Multivariate exploratory tools for microarray data analysis. Biostatistics 2003, 4(4):555-567. 10.1093/biostatistics/4.4.555, 14557111.
-
(2003)
Biostatistics
, vol.4
, Issue.4
, pp. 555-567
-
-
Szabo, A.1
Boucher, K.2
Jones, D.3
Tsodikov, A.D.4
Klebanov, L.E.V.B.5
Yakovlev, A.Y.6
-
24
-
-
25444472585
-
Pathway level analysis of gene expression using singular value decomposition
-
10.1186/1471-2105-6-225, 1261155, 16156896
-
Tomfohr J, Lu J, Kepler TB. Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics 2005, 6:225. 10.1186/1471-2105-6-225, 1261155, 16156896.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 225
-
-
Tomfohr, J.1
Lu, J.2
Kepler, T.B.3
-
25
-
-
63449107173
-
A general modular framework for gene set enrichment analysis
-
10.1186/1471-2105-10-47, 2661051, 19192285
-
Ackermann M, Strimmer K. A general modular framework for gene set enrichment analysis. BMC Bioinformatics 2009, 10(1):47. 10.1186/1471-2105-10-47, 2661051, 19192285.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.1
, pp. 47
-
-
Ackermann, M.1
Strimmer, K.2
-
26
-
-
4544341015
-
Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
-
Smyth GK. Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Statistical Applications in Genetics and Molecular Biology 2004, 3(1):1027.
-
(2004)
Statistical Applications in Genetics and Molecular Biology
, vol.3
, Issue.1
, pp. 1027
-
-
Smyth, G.K.1
-
28
-
-
0037076272
-
Diagnosis of multiple cancer types by shrunken centroids of gene expression
-
Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proceedings of the National Academy of Sciences 2002, 99(10):6567-6572.
-
(2002)
Proceedings of the National Academy of Sciences
, vol.99
, Issue.10
, pp. 6567-6572
-
-
Tibshirani, R.1
Hastie, T.2
Narasimhan, B.3
Chu, G.4
-
29
-
-
34547483895
-
Improving gene set analysis of microarray data by SAM-GS
-
10.1186/1471-2105-8-242, 1931607, 17612399
-
Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, Yasui Y. Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics 2007, 8:242. 10.1186/1471-2105-8-242, 1931607, 17612399.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 242
-
-
Dinu, I.1
Potter, J.D.2
Mueller, T.3
Liu, Q.4
Adewale, A.J.5
Jhangri, G.S.6
Einecke, G.7
Famulski, K.S.8
Halloran, P.9
Yasui, Y.10
-
30
-
-
24144445705
-
Improved statistical tests for differential gene expression by shrinking variance components estimates
-
10.1093/biostatistics/kxh018, 15618528
-
Cui X, Hwang JT, Qiu J, Blades NJ, Churchill GA. Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 2005, 6(1):59-75. 10.1093/biostatistics/kxh018, 15618528.
-
(2005)
Biostatistics
, vol.6
, Issue.1
, pp. 59-75
-
-
Cui, X.1
Hwang, J.T.2
Qiu, J.3
Blades, N.J.4
Churchill, G.A.5
-
31
-
-
63549122405
-
Multivariate analysis of variance test for gene set analysis
-
10.1093/bioinformatics/btp098, 19254923
-
Tsai C, Chen J. Multivariate analysis of variance test for gene set analysis. Bioinformatics 2009, 25(7):897-903. 10.1093/bioinformatics/btp098, 19254923.
-
(2009)
Bioinformatics
, vol.25
, Issue.7
, pp. 897-903
-
-
Tsai, C.1
Chen, J.2
-
32
-
-
33745156863
-
Some theory for Fisher's linear discriminant function,"naive Bayes", and some alternatives when there are many more variables than observations
-
Bickel PJ, Levina E. Some theory for Fisher's linear discriminant function,"naive Bayes", and some alternatives when there are many more variables than observations. Bernoulli 2004, 10(6):989-1010.
-
(2004)
Bernoulli
, vol.10
, Issue.6
, pp. 989-1010
-
-
Bickel, P.J.1
Levina, E.2
-
33
-
-
41549106844
-
Regularized estimation of large covariance matrices
-
Bickel PJ, Levina E. Regularized estimation of large covariance matrices. Annals of Statistics 2008, 36(1):199-227.
-
(2008)
Annals of Statistics
, vol.36
, Issue.1
, pp. 199-227
-
-
Bickel, P.J.1
Levina, E.2
|