-
1
-
-
63449107173
-
A general modular framework for gene set enrichment analysis
-
Ackermann M, Strimmer K. 2009. A general modular framework for gene set enrichment analysis. BMC Bioinformatics 10:47.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 47
-
-
Ackermann, M.1
Strimmer, K.2
-
2
-
-
0034730140
-
Singular value decomposition for genomewide expression data processing and modeling
-
USA
-
Alter O, Brown PO, Botstein D. 2000. Singular value decomposition for genomewide expression data processing and modeling. P Natl Acad Sci USA 97:10101-10106.
-
(2000)
P Natl Acad Sci
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
Brown, P.O.2
Botstein, D.3
-
3
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
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. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29. (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, 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..
-
4
-
-
0001677717
-
Controlling the false discovery rate - A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Roy Stat Soc B 57:289-300.
-
(1995)
J Roy Stat Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
5
-
-
54949127956
-
Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes
-
Chen X, Wang L, Smith JD, Zhang B 2008. Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics 24:2474-2481.
-
(1995)
Bioinformatics
, vol.24
, pp. 2474-2481
-
-
Chen, X.1
Wang, L.2
Smith, J.D.3
Zhang, B.4
-
6
-
-
77958611364
-
Pathway-based analysis for genome-wide association studies using supervised principal components
-
Chen X, Wang L, Hu B, Guo M, Barnard J, Zhu X. 2010. Pathway-based analysis for genome-wide association studies using supervised principal components. Genet Epidemiol 34:716-724.
-
(2010)
Genet Epidemiol
, vol.34
, pp. 716-724
-
-
Chen, X.1
Wang, L.2
Hu, B.3
Guo, M.4
Barnard, J.5
Zhu, X.6
-
7
-
-
40849147041
-
Drug therapy: EGFR antagonists in cancer treatment
-
Ciardiello F, Tortora G. 2008. Drug therapy: EGFR antagonists in cancer treatment. New Engl J Med 358:1160-1174.
-
(2008)
New Engl J Med
, vol.358
, pp. 1160-1174
-
-
Ciardiello, F.1
Tortora, G.2
-
8
-
-
34547483895
-
Improving gene set analysis of microarray data by SAM-GS
-
Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, Yasui Y. 2007. Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics 8:242.
-
(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
-
10
-
-
35348890683
-
On testing the significance of sets of genes
-
Efron B, Tibshirani R. 2007. On testing the significance of sets of genes. Ann Appl Stat 1:107-129.
-
(2007)
Ann Appl Stat
, vol.1
, pp. 107-129
-
-
Efron, B.1
Tibshirani, R.2
-
12
-
-
33747028745
-
Anticancer drug clustering in lung cancer based on gene expression profiles and sensitivity database
-
Gemma A, Li C, Sugiyama Y, Matsuda K, Seike Y, Kosaihira S, Minegishi Y, Noro R, Nara M, Seike M, Yoshimura A, Shionoya A, Kawakami A, Ogawa N, Uesaka H, Kudoh S. 2006. Anticancer drug clustering in lung cancer based on gene expression profiles and sensitivity database. BMC Cancer 6:174.
-
(2006)
BMC Cancer
, vol.6
, pp. 174
-
-
Gemma, A.1
Li, C.2
Sugiyama, Y.3
Matsuda, K.4
Seike, Y.5
Kosaihira, S.6
Minegishi, Y.7
Noro, R.8
Nara, M.9
Seike, M.10
Yoshimura, A.11
Shionoya, A.12
Kawakami, A.13
Ogawa, N.14
Uesaka, H.15
Kudoh, S.16
-
13
-
-
0345832338
-
A global test for groups fo genes: Testing association with a clinical outcome
-
DOI 10.1093/bioinformatics/btg382
-
Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC 2004. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 20:93-99. (Pubitemid 38088346)
-
(2004)
Bioinformatics
, vol.20
, Issue.1
, pp. 93-99
-
-
Goeman, J.J.1
Van De Geer, S.2
De Kort, F.3
Van Houwellingen, H.C.4
-
14
-
-
34249663294
-
Analyzing gene expression data in terms of gene sets: Methodological issues
-
DOI 10.1093/bioinformatics/btm051
-
Goeman JJ, Buhlmann P 2007. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23:980-987. (Pubitemid 47050585)
-
(2007)
Bioinformatics
, vol.23
, Issue.8
, pp. 980-987
-
-
Goeman, J.J.1
Buhlmann, P.2
-
15
-
-
77958502224
-
The renin-Angiotensin system and cancer: Old dog, new tricks
-
George AJ, Thomas WG, Hannan RD 2010. The renin-angiotensin system and cancer: old dog, new tricks. Nat Rev Cancer 10:745-759.
-
(2010)
Nat Rev Cancer
, vol.10
, pp. 745-759
-
-
George, A.J.1
Thomas, W.G.2
Hannan, R.D.3
-
16
-
-
0035839608
-
Target genes of peroxisome proliferator-activated receptor gamma in colorectal cancer cells
-
Gupta RA, Brockman JA, Sarraf P, Willson TM, DuBois RN 2001. Target genes of peroxisome proliferator-activated receptor gamma in colorectal cancer cells. J Biol Chem 276:29681-29687.
-
(2001)
J Biol Chem
, vol.276
, pp. 29681-29687
-
-
Gupta, R.A.1
Brockman, J.A.2
Sarraf, P.3
Willson, T.M.4
DuBois, R.N.5
-
17
-
-
1942470331
-
Activation of nuclear hormone receptor peroxisome proliferator-activated receptor-δ accelerates intestinal adenoma growth
-
DOI 10.1038/nm993
-
Gupta RA, Wang DZ, Katkuri S, Wang HB, Dey SK, DuBois R.N. 2004. Activation of nuclear hormone receptor peroxisome proliferator-activated receptor-delta accelerates intestinal adenoma growth. Nat Med 10:245-247. (Pubitemid 38667613)
-
(2004)
Nature Medicine
, vol.10
, Issue.3
, pp. 245-247
-
-
Gupta, R.A.1
Wang, D.2
Katkuri, S.3
Wang, H.4
Dey, S.K.5
DuBois, R.N.6
-
18
-
-
37549057612
-
GlobalANCOVA: Exploration and assessment of gene group effects
-
Hummel M, Meister R, Mansmann U 2008. GlobalANCOVA: exploration and assessment of gene group effects. Bioinformatics 24:78-85.
-
(2008)
Bioinformatics
, vol.24
, pp. 78-85
-
-
Hummel, M.1
Meister, R.2
Mansmann, U.3
-
19
-
-
13444300936
-
The Wnt/β-catenin signaling pathway targets PPARγ activity in colon cancer cells
-
DOI 10.1073/pnas.0405928102
-
Jansson EA, Are A, Greicius G, Kuo IC, Kelly D, Arulampalam V, Pettersson S 2005. The Wnt/beta-catenin signaling pathway targets PPAR gamma activity in colon cancer cells. P Natl Acad Sci USA 102:1460-1465. (Pubitemid 40209192)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.5
, pp. 1460-1465
-
-
Jansson, E.A.1
Are, A.2
Greicius, G.3
Kuo, I.-C.4
Kelly, D.5
Arulampalam, V.6
Pettersson, S.7
-
20
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Kanehisa M, Goto S 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27-30. (Pubitemid 30047706)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
21
-
-
33750007469
-
A multivariate approach for integrating genome-wide expression data and biological knowledge
-
DOI 10.1093/bioinformatics/btl401
-
Kong SW, Pu WT, Park PJ 2006. A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics 22:2373-2380. (Pubitemid 44566966)
-
(2006)
Bioinformatics
, vol.22
, Issue.19
, pp. 2373-2380
-
-
Kong, S.W.1
Pu, W.T.2
Park, P.J.3
-
22
-
-
64849105122
-
On general adaptive sparse principal component analysis
-
Leng C, Wang H 2009. On General Adaptive Sparse Principal Component Analysis. J Comput Graph Stat 18:201-215.
-
(2009)
J Comput Graph Stat
, vol.18
, pp. 201-215
-
-
Leng, C.1
Wang, H.2
-
23
-
-
33646228635
-
KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer
-
Lièvre A, Bachet JB, Le Corre D, Boige V, Landi B., Emile J.F., Cote J.F., Tomasic G., Penna C., Ducreux M., Rougier P., Penault-Llorca F., Laurent-Puig P. 2006. KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer. Cancer Res 66:3992-3995.
-
(2006)
Cancer Res
, vol.66
, pp. 3992-3995
-
-
Lièvre, A.1
Bachet, J.B.2
Le Corre, D.3
Boige, V.4
Landi, B.5
Emile, J.F.6
Cote, J.F.7
Tomasic, G.8
Penna, C.9
Ducreux, M.10
Rougier, P.11
Penault-Llorca, F.12
Laurent-Puig, P.13
-
24
-
-
38949165049
-
Comparative evaluation of gene-set analysis methods
-
Liu Q, Dinu I, Adewale AJ, Potter JD, Yasui Y. 2007. Comparative evaluation of gene-set analysis methods. BMC Bioinformatics 8:431
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 431
-
-
Liu, Q.1
Dinu, I.2
Adewale, A.J.3
Potter, J.D.4
Yasui, Y.5
-
25
-
-
63549098588
-
Identification of differential gene pathways with principal component analysis
-
Ma S, Kosorok MR. 2009. Identification of differential gene pathways with principal component analysis. Bioinformatics 25:882-889.
-
(2009)
Bioinformatics
, vol.25
, pp. 882-889
-
-
Ma, S.1
Kosorok, M.R.2
-
26
-
-
0038054341
-
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
-
DOI 10.1038/ng1180
-
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. 2003. PGC-1 alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34:267-273. (Pubitemid 36792858)
-
(2003)
Nature Genetics
, 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
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..
-
27
-
-
43149116763
-
Gene-set approach for expression pattern analysis
-
DOI 10.1093/bib/bbn001
-
Nam D, Kim SY. 2008. Gene-set approach for expression pattern analysis. Brief Bioinform 9:189-197. (Pubitemid 351637941)
-
(2008)
Briefings in Bioinformatics
, vol.9
, Issue.3
, pp. 189-197
-
-
Nam, D.1
Kim, S.-Y.2
-
28
-
-
43049086717
-
Sparse principal component analysis via regularized low rank matrix approximation
-
Shen HP, Huang JHZ. 2008. Sparse principal component analysis via regularized low rank matrix approximation. J Multivariate Anal 99:1015-1034.
-
(2008)
J Multivariate Anal
, vol.99
, pp. 1015-1034
-
-
Shen, H.P.1
Huang, J.H.Z.2
-
29
-
-
77249143960
-
Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer
-
Smith JJ, Deane NG, Wu F, Merchant NB, Zhang B, Jiang AX, Lu PC, Johnson JC, Schmidt C, Bailey CE, Eschrich S, Kis C, Levy S, Washington MK, Heslin MJ, Coffey RJ, Yeatman TJ, Shyr Y, Beauchamp RD. 2010. Experimentally Derived Metastasis Gene Expression Profile Predicts Recurrence and Death in Patients With Colon Cancer. Gastroenterology 138:958-968.
-
(2010)
Gastroenterology
, vol.138
, pp. 958-968
-
-
Smith, J.J.1
Deane, N.G.2
Wu, F.3
Merchant, N.B.4
Zhang, B.5
Jiang, A.X.6
Lu, P.C.7
Johnson, J.C.8
Schmidt, C.9
Bailey, C.E.10
Eschrich, S.11
Kis, C.12
Levy, S.13
Washington, M.K.14
Heslin, M.J.15
Coffey, R.J.16
Yeatman, T.J.17
Shyr, Y.18
Beauchamp, R.D.19
-
30
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
DOI 10.1073/pnas.0506580102
-
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. 2005. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. P Natl Acad Sci USA 102:15545-15550. (Pubitemid 41528093)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, 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
-
31
-
-
0001287271
-
Regression shrinkage and selection via the Lasso
-
Tibshirani R. 1996. Regression shrinkage and selection via the Lasso. J Roy Stat Soc B 58:267-288.
-
(1996)
J Roy Stat Soc B
, vol.58
, pp. 267-288
-
-
Tibshirani, R.1
-
32
-
-
25444472585
-
Pathway level analysis of gene expression using singular value decomposition
-
Tomfohr J, Lu J, Kepler TB. 2005. Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics 6:225.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 225
-
-
Tomfohr, J.1
Lu, J.2
Kepler, T.B.3
-
33
-
-
63549122405
-
Multivariate analysis of variance test for gene set analysis
-
Tsai CA, Chen JJ. 2009. Multivariate analysis of variance test for gene set analysis. Bioinformatics 25:897-903.
-
(2009)
Bioinformatics
, vol.25
, pp. 897-903
-
-
Tsai, C.A.1
Chen, J.J.2
-
34
-
-
35348879976
-
Unified LASSO estimation by least squares approximation
-
Wang H, Leng C. 2007. Unified LASSO estimation by least squares approximation. J Am Stat Assoc 102:1039-1048.
-
(2007)
J Am Stat Assoc
, vol.102
, pp. 1039-1048
-
-
Wang, H.1
Leng, C.2
-
35
-
-
48249108773
-
An integrated approach for the analysis of biological pathways using mixed models
-
Wang L, Zhang B, Wolfinger RD, Chen X. 2008. An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet 4:e1000115.
-
(2008)
PLoS Genet
, vol.4
-
-
Wang, L.1
Zhang, B.2
Wolfinger, R.D.3
Chen, X.4
-
36
-
-
73849140082
-
A unified mixed effects model for gene set analysis of time course microarray experiments
-
Wang L, Chen X, Wolfinger RD, Franklin JL, Coffey RJ, Zhang B. 2009. A unified mixed effects model for gene set analysis of time course microarray experiments. Stat Appl Genet Mol Biol 8:47.
-
(2009)
Stat Appl Genet Mol Biol
, vol.8
, pp. 47
-
-
Wang, L.1
Chen, X.2
Wolfinger, R.D.3
Franklin, J.L.4
Coffey, R.J.5
Zhang, B.6
-
37
-
-
0034594870
-
A nuclear receptor to prevent colon cancer
-
DOI 10.1056/NEJM200003023420909
-
Wu GD. 2000. A nuclear receptor to prevent colon cancer. New Engl J Med 342:651-653. (Pubitemid 30118420)
-
(2000)
New England Journal of Medicine
, vol.342
, Issue.9
, pp. 651-653
-
-
Wu, G.D.1
|