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Volumn 6, Issue 2, 2012, Pages 561-600

More power via graph-structured tests for differential expression of gene networks

Author keywords

Biological networks; Differential expression; Dimensionality reduction; Enrichment analysis; Graph laplacian; Hotelling T2; Pathways; Spectral graph theory; Two sample test

Indexed keywords


EID: 84866238676     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/11-AOAS528     Document Type: Article
Times cited : (65)

References (76)
  • 2
    • 2142645905 scopus 로고    scopus 로고
    • Effect of high dimension: By an example of a two sample problem
    • MR1399305
    • BAI, Z. and SARANADASA, H. (1996). Effect of high dimension: By an example of a two sample problem. Statist. Sinica 6 311-329. MR1399305
    • (1996) Statist. Sinica , vol.6 , pp. 311-329
    • Bai, Z.1    Saranadasa, H.2
  • 4
    • 0030980877 scopus 로고    scopus 로고
    • Cyclin D1 in mammary carcinoma
    • BARNES, D. M. (1997). Cyclin D1 in mammary carcinoma. J. Pathol. 181 267-269.
    • (1997) J. Pathol , vol.181 , pp. 267-269
    • Barnes, D.M.1
  • 5
    • 3142665525 scopus 로고    scopus 로고
    • GOstat: Find statistically overrepresented Gene Ontologies within a group of genes
    • BEISSBARTH, T. and SPEED, T. P. (2004). GOstat: Find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20 1464-1465.
    • (2004) Bioinformatics , vol.20 , pp. 1464-1465
    • Beissbarth, T.1    Speed, T.P.2
  • 6
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • MR1325392
    • BENJAMINI, Y. and HOCHBERG, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57 289-300. MR1325392
    • (1995) J. Roy. Statist. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 7
    • 77649330805 scopus 로고    scopus 로고
    • A two-sample test for high-dimensional data with applications to gene-set testing
    • MR2604697
    • CHEN, S. X. and QIN, Y.-L. (2010). A two-sample test for high-dimensional data with applications to gene-set testing. Ann. Statist. 38 808-835. MR2604697
    • (2010) Ann. Statist , vol.38 , pp. 808-835
    • Chen, S.X.1    Qin, Y.-L.2
  • 8
    • 70349952418 scopus 로고    scopus 로고
    • Cell cycle genes and ovarian cancer susceptibility: A tagSNP analysis
    • Ovarian Cancer Association Consortium
    • CUNNINGHAM, J. M., VIERKANT, R. A., SELLERS, T. A., PHELAN, C., RIDER, D. N., LIEBOW, M., SCHILDKRAUT, J., BERCHUCK, A., COUCH, F. J., WANG, X., FRIDLEY, B. L., Ovarian Cancer Association Consortium, GENTRY MAHARAJ, A., MENON, U., HOGDALL, E., KJAER, S., WHITTEMORE, A., DICIOCCIO, R., SONG, H., GAYTHER, S. A., RAMUS, S. J., PHARAOH, P. D. P. and GOODE, E. L. (2009). Cell cycle genes and ovarian cancer susceptibility: A tagSNP analysis. Br. J. Cancer 101 1461-1468.
    • (2009) Br. J. Cancer , vol.101 , pp. 1461-1468
    • Cunningham, J.M.1    Vierkant, R.A.2    Sellers, T.A.3    Phelan, C.4    Rider, D.N.5    Liebow, M.6    Schildkraut, J.7    Berchuck, A.8    Couch, F.J.9    Wang, X.10    Fridley, B.L.11
  • 9
    • 0011658543 scopus 로고
    • Power of the noncentral F test: Effect of additional variates on Hotelling's T 2-test
    • DAS GUPTA, S. and PERLMAN, M. D. (1974). Power of the noncentral F test: Effect of additional variates on Hotelling's T 2-test. J. Amer. Statist. Assoc. 69 174-180.
    • (1974) J. Amer. Statist. Assoc , vol.69 , pp. 174-180
    • das Gupta, S.1    Perlman, M.D.2
  • 10
    • 84968511079 scopus 로고
    • Some new bounds on perturbation of subspaces
    • MR0246155
    • DAVIS, C. and KAHAN, W. M. (1969). Some new bounds on perturbation of subspaces. Bull. Amer. Math. Soc. 75 863-868. MR0246155
    • (1969) Bull. Amer. Math. Soc , vol.75 , pp. 863-868
    • Davis, C.1    Kahan, W.M.2
  • 12
    • 0030727705 scopus 로고    scopus 로고
    • Dietary restriction reduces insulin-like growth factor I levels, which modulates apoptosis, cell proliferation, and tumor progression in p53-deficient mice
    • DUNN, S. E., KARI, F. W., FRENCH, J., LEININGER, J. R., TRAVLOS, G., WILSON, R. and BARRETT, J. C. (1997). Dietary restriction reduces insulin-like growth factor I levels, which modulates apoptosis, cell proliferation, and tumor progression in p53-deficient mice. Cancer Res. 57 4667-4672.
    • (1997) Cancer Res , vol.57 , pp. 4667-4672
    • Dunn, S.E.1    Kari, F.W.2    French, J.3    Leininger, J.R.4    Travlos, G.5    Wilson, R.6    Barrett, J.C.7
  • 13
    • 13444282534 scopus 로고    scopus 로고
    • Outcome signature genes in breast cancer: Is there a unique set?
    • EIN-DOR, L., KELA, I., GETZ, G., GIVOL, D. and DOMANY, E. (2005). Outcome signature genes in breast cancer: Is there a unique set? Bioinformatics 21 171-178.
    • (2005) Bioinformatics , vol.21 , pp. 171-178
    • Ein-Dor, L.1    Kela, I.2    Getz, G.3    Givol, D.4    Domany, E.5
  • 15
    • 0003448545 scopus 로고    scopus 로고
    • Graduate Studies in Mathematics 19. Amer. Math. Soc., Providence, RI. MR1625845
    • EVANS, L. C. (1998). Partial Differential Equations. Graduate Studies in Mathematics 19. Amer. Math. Soc., Providence, RI. MR1625845
    • (1998) Partial Differential Equations
    • Evans, L.C.1
  • 16
    • 0032332076 scopus 로고    scopus 로고
    • Test of significance when data are curves
    • MR1649196
    • FAN, J. and LIN, S.-K. (1998). Test of significance when data are curves. J. Amer. Statist. Assoc. 93 1007-1021. MR1649196
    • (1998) J. Amer. Statist. Assoc , vol.93 , pp. 1007-1021
    • Fan, J.1    Lin, S.-K.2
  • 17
    • 79951978817 scopus 로고    scopus 로고
    • P53 status influences response to tamoxifen but not to fulvestrant in breast cancer cell lines
    • FERNANDEZ-CUESTA, L., ANAGANTI, S., HAINAUT, P. and OLIVIER, M. (2010). P53 status influences response to tamoxifen but not to fulvestrant in breast cancer cell lines. Int. J. Cancer 128 1813-1821.
    • (2010) Int. J. Cancer , vol.128 , pp. 1813-1821
    • Fernandez-Cuesta, L.1    Anaganti, S.2    Hainaut, P.3    Olivier, M.4
  • 18
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: Methodological issues
    • GOEMAN, J. J. and BÜHLMANN, P. (2007). Analyzing gene expression data in terms of gene sets: Methodological issues. Bioinformatics 23 980-987.
    • (2007) Bioinformatics , vol.23 , pp. 980-987
    • Goeman, J.J.1    Bühlmann, P.2
  • 20
    • 17844398046 scopus 로고    scopus 로고
    • Molecular changes in tamoxifenresistant breast cancer: Relationship between estrogen receptor, HER-2, and p38 mitogenactivated protein kinase
    • GUTIERREZ, M. C., DETRE, S., JOHNSTON, S., MOHSIN, S. K., SHOU, J., ALLRED, D. C., SCHIFF, R., OSBORNE, C. K. and DOWSETT, M. (2005). Molecular changes in tamoxifenresistant breast cancer: Relationship between estrogen receptor, HER-2, and p38 mitogenactivated protein kinase. J. Clin. Oncol. 23 2469-2476.
    • (2005) J. Clin. Oncol , vol.23 , pp. 2469-2476
    • Gutierrez, M.C.1    Detre, S.2    Johnston, S.3    Mohsin, S.K.4    Shou, J.5    Allred, D.C.6    Schiff, R.7    Osborne, C.K.8    Dowsett, M.9
  • 22
    • 83755163963 scopus 로고    scopus 로고
    • The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures
    • arXiv:1101.5008
    • HAURY, A. C., GESTRAUD, P. and VERT, J. P. (2011). The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures. Preprint. Available at arXiv:1101.5008.
    • (2011) Preprint
    • Haury, A.C.1    Gestraud, P.2    Vert, J.P.3
  • 26
    • 33846235881 scopus 로고    scopus 로고
    • Cooperative action of tamoxifen and c-Src inhibition in preventing the growth of estrogen receptor-positive human breast cancer cells
    • HERYNK, M. H., BEYER, A. R., CUI, Y., WEISS, H., ANDERSON, E., GREEN, T. P. and FUQUA, S. A. W. (2006). Cooperative action of tamoxifen and c-Src inhibition in preventing the growth of estrogen receptor-positive human breast cancer cells. Mol. Cancer Ther. 5 3023-3031.
    • (2006) Mol. Cancer Ther , vol.5 , pp. 3023-3031
    • Herynk, M.H.1    Beyer, A.R.2    Cui, Y.3    Weiss, H.4    Anderson, E.5    Green, T.P.6    Fuqua, S.A.W.7
  • 27
    • 43449101852 scopus 로고    scopus 로고
    • Molecular profiling of bladder cancer: Involvement of the TGF-beta pathway in bladder cancer progression
    • HUNG, T.-T., WANG, H., KINGSLEY, E. A., RISBRIDGER, G. P. and RUSSELL, P. J. (2008). Molecular profiling of bladder cancer: Involvement of the TGF-beta pathway in bladder cancer progression. Cancer Lett. 265 27-38.
    • (2008) Cancer Lett , vol.265 , pp. 27-38
    • Hung, T.-T.1    Wang, H.2    Kingsley, E.A.3    Risbridger, G.P.4    Russell, P.J.5
  • 29
    • 84866253834 scopus 로고    scopus 로고
    • The eigenproblem and invariant subspaces: Perturbation theory
    • M. E. Kilmer and D. P. O'Leary, eds.), Birkhäuser, Basel. MR2731855
    • IPSEN, I. C. F. (2010). The eigenproblem and invariant subspaces: Perturbation theory. In G. W. Stewart: Selected Works with Commentaries (M. E. Kilmer and D. P. O'Leary, eds.) 71-93. Birkhäuser, Basel. MR2731855
    • (2010) G. W. Stewart: Selected Works With Commentaries , pp. 71-93
    • Ipsen, I.C.F.1
  • 36
    • 75549090821 scopus 로고    scopus 로고
    • Pre-clinical evaluation of cyclin-dependent kinase 2 and 1 inhibition in anti-estrogen-sensitive and resistant breast cancer cells
    • JOHNSON, N., BENTLEY, J., WANG, L.-Z., NEWELL, D. R., ROBSON, C. N., SHAPIRO, G. I. and CURTIN, N. J. (2010). Pre-clinical evaluation of cyclin-dependent kinase 2 and 1 inhibition in anti-estrogen-sensitive and resistant breast cancer cells. Br. J. Cancer 102 342-350.
    • (2010) Br. J. Cancer , vol.102 , pp. 342-350
    • Johnson, N.1    Bentley, J.2    Wang, L.-Z.3    Newell, D.R.4    Robson, C.N.5    Shapiro, G.I.6    Curtin, N.J.7
  • 37
    • 33644868287 scopus 로고    scopus 로고
    • Molecular subtypes of bladder cancer: Jekyll and Hyde or chalk and cheese?
    • KNOWLES, M. A. (2006). Molecular subtypes of bladder cancer: Jekyll and Hyde or chalk and cheese? Carcinogenesis 27 361-373.
    • (2006) Carcinogenesis , vol.27 , pp. 361-373
    • Knowles, M.A.1
  • 38
    • 0001173632 scopus 로고
    • An automatic method of solving discrete programming problems
    • MR0115825
    • LAND, A. H. and DOIG, A. G. (1960). An automatic method of solving discrete programming problems. Econometrica 28 497-520. MR0115825
    • (1960) Econometrica , vol.28 , pp. 497-520
    • Land, A.H.1    Doig, A.G.2
  • 41
    • 0036012343 scopus 로고    scopus 로고
    • Replicated microarray data
    • MR1894187
    • LÖNNSTEDT, I. and SPEED, T. (2002). Replicated microarray data. Statist. Sinica 12 31-46. MR1894187
    • (2002) Statist. Sinica , vol.12 , pp. 31-46
    • Lönnstedt, I.1    Speed, T.2
  • 43
    • 77949753453 scopus 로고    scopus 로고
    • Estrogen receptor regulates E2F1 expression to mediate tamoxifen resistance
    • LOUIE, M. C., MCCLELLAN, A., SIEWIT, C. and KAWABATA, L. (2010). Estrogen receptor regulates E2F1 expression to mediate tamoxifen resistance. Mol. Cancer Res. 8 343-352.
    • (2010) Mol. Cancer Res , vol.8 , pp. 343-352
    • Louie, M.C.1    McClellan, A.2    Siewit, C.3    Kawabata, L.4
  • 44
    • 25144474547 scopus 로고    scopus 로고
    • Hotelling's T 2 multivariate profiling for detecting differential expression in microarrays
    • LU, Y., LIU, P.-Y., XIAO, P. and DENG, H.-W. (2005). Hotelling's T 2 multivariate profiling for detecting differential expression in microarrays. Bioinformatics 21 3105-3113.
    • (2005) Bioinformatics , vol.21 , pp. 3105-3113
    • Lu, Y.1    Liu, P.-Y.2    Xiao, P.3    Deng, H.-W.4
  • 45
    • 0035863425 scopus 로고    scopus 로고
    • Inhibiting mutations in the transforming growth factor beta type 2 receptor in recurrent human breast cancer
    • LÜCKE, C. D., PHILPOTT, A., METCALFE, J. C., THOMPSON, A. M., HUGHES-DAVIES, L., KEMP, P. R. and HESKETH, R. (2001). Inhibiting mutations in the transforming growth factor beta type 2 receptor in recurrent human breast cancer. Cancer Res. 61 482-485.
    • (2001) Cancer Res , vol.61 , pp. 482-485
    • Lücke, C.D.1    Philpott, A.2    Metcalfe, J.C.3    Thompson, A.M.4    Hughes-Davies, L.5    Kemp, P.R.6    Hesketh, R.7
  • 46
    • 63549098588 scopus 로고    scopus 로고
    • Identification of differential gene pathways with principal component analysis
    • MA, S. and KOSOROK, M. R. (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
  • 47
    • 77952138750 scopus 로고    scopus 로고
    • Aberrant leukocyte infiltration: A direct trigger for breast tumor invasion and metastasis
    • MAN, Y.-G. (2010). Aberrant leukocyte infiltration: A direct trigger for breast tumor invasion and metastasis. Int. J. Biol. Sci. 6 129-132.
    • (2010) Int. J. Biol. Sci , vol.6 , pp. 129-132
    • Man, Y.-G.1
  • 49
    • 0029655413 scopus 로고    scopus 로고
    • C-erbB-2 in bladder cancer: Molecular biology, correlation with epidermal growth factor receptors and prognostic value
    • MELLON, J. K., LUNEC, J., WRIGHT, C., HORNE, C. H., KELLY, P. and NEAL, D. E. (1996). C-erbB-2 in bladder cancer: Molecular biology, correlation with epidermal growth factor receptors and prognostic value. J. Urol. 155 321-326.
    • (1996) J. Urol , vol.155 , pp. 321-326
    • Mellon, J.K.1    Lunec, J.2    Wright, C.3    Horne, C.H.4    Kelly, P.5    Neal, D.E.6
  • 51
    • 69249137029 scopus 로고    scopus 로고
    • Biological determinants of endocrine resistance in breast cancer
    • MUSGROVE, E. A. and SUTHERLAND, R. L. (2009). Biological determinants of endocrine resistance in breast cancer. Nat. Rev. Cancer 9 631-643.
    • (2009) Nat. Rev. Cancer , vol.9 , pp. 631-643
    • Musgrove, E.A.1    Sutherland, R.L.2
  • 52
    • 34248593385 scopus 로고    scopus 로고
    • Gene expression network analysis and applications to immunology
    • NACU, S., CRITCHLEY-THORNE, R., LEE, P. and HOLMES, S. (2007). Gene expression network analysis and applications to immunology. Bioinformatics 23 850.
    • (2007) Bioinformatics , vol.23 , pp. 850
    • Nacu, S.1    Critchley-Thorne, R.2    Lee, P.3    Holmes, S.4
  • 57
    • 25144504517 scopus 로고    scopus 로고
    • Expression of mucins (MUC1, MUC2, MUC3, MUC4, MUC5AC and MUC6) and their prognostic significance in human breast cancer
    • RAKHA, E. A., BOYCE, R. W. G., EL-REHIM, D. A., KURIEN, T., GREEN, A. R., PAISH, E. C., ROBERTSON, J. F. R. and ELLIS, I. O. (2005). Expression of mucins (MUC1, MUC2, MUC3, MUC4, MUC5AC and MUC6) and their prognostic significance in human breast cancer. Mod. Pathol. 18 1295-1304.
    • (2005) Mod. Pathol , vol.18 , pp. 1295-1304
    • Rakha, E.A.1    Boyce, R.W.G.2    El-Rehim, D.A.3    Kurien, T.4    Green, A.R.5    Paish, E.C.6    Robertson, J.F.R.7    Ellis, I.O.8
  • 59
    • 32944455363 scopus 로고    scopus 로고
    • Levels of IL-1 beta control stimulatory/inhibitory growth of cancer cells
    • ROY, D., SARKAR, S. and FELTY, Q. (2006). Levels of IL-1 beta control stimulatory/inhibitory growth of cancer cells. Front. Biosci. 11 889-898.
    • (2006) Front. Biosci , vol.11 , pp. 889-898
    • Roy, D.1    Sarkar, S.2    Felty, Q.3
  • 60
    • 33644867290 scopus 로고    scopus 로고
    • Defining molecular profiles of poor outcome in patients with invasive bladder cancer using oligonucleotide microarrays
    • SANCHEZ-CARBAYO, M., SOCCI, N. D., LOZANO, J., SAINT, F. and CORDON-CARDO, C. (2006). Defining molecular profiles of poor outcome in patients with invasive bladder cancer using oligonucleotide microarrays. J. Clin. Oncol. 24 778-789.
    • (2006) J. Clin. Oncol , vol.24 , pp. 778-789
    • Sanchez-Carbayo, M.1    Socci, N.D.2    Lozano, J.3    Saint, F.4    Cordon-Cardo, C.5
  • 64
    • 57449095509 scopus 로고    scopus 로고
    • A test for the mean vector with fewer observations than the dimension under nonnormality
    • MR2483435
    • SRIVASTAVA, M. S. (2009). A test for the mean vector with fewer observations than the dimension under nonnormality. J. Multivariate Anal. 100 518-532. MR2483435
    • (2009) J. Multivariate Anal , vol.100 , pp. 518-532
    • Srivastava, M.S.1
  • 65
    • 38349085267 scopus 로고    scopus 로고
    • A test for the mean vector with fewer observations than the dimension
    • MR2396970
    • SRIVASTAVA, M. S. and DU, M. (2008). A test for the mean vector with fewer observations than the dimension. J. Multivariate Anal. 99 386-402. MR2396970
    • (2008) J. Multivariate Anal , vol.99 , pp. 386-402
    • Srivastava, M.S.1    Du, M.2
  • 69
    • 77954571810 scopus 로고    scopus 로고
    • CDK inhibitors as potential breast cancer therapeutics: New evidence for enhanced efficacy in ER+ disease
    • SUTHERLAND, R. L. and MUSGROVE, E. A. (2009). CDK inhibitors as potential breast cancer therapeutics: New evidence for enhanced efficacy in ER+ disease. Breast Cancer Res. 11 112.
    • (2009) Breast Cancer Res , vol.11 , pp. 112
    • Sutherland, R.L.1    Musgrove, E.A.2
  • 70
    • 62949237566 scopus 로고    scopus 로고
    • On gene ranking using replicated microarray time course data
    • MR2665844
    • TAI, Y. C. and SPEED, T. P. (2009). On gene ranking using replicated microarray time course data. Biometrics 65 40-51. MR2665844
    • (2009) Biometrics , vol.65 , pp. 40-51
    • Tai, Y.C.1    Speed, T.P.2
  • 73
    • 78650280312 scopus 로고    scopus 로고
    • Algorithms for detecting significantly mutated pathways in cancer
    • In RECOMB (B. Berger, ed.), Springer, Berlin
    • VANDIN, F., UPFAL, E. and RAPHAEL, B. J. (2010). Algorithms for detecting significantly mutated pathways in cancer. In RECOMB (B. Berger, ed.). Lecture Notes in Computer Science 6044 506-521. Springer, Berlin.
    • (2010) Lecture Notes In Computer Science , vol.6044 , pp. 506-521
    • Vandin, F.1    Upfal, E.2    Raphael, B.J.3
  • 76
    • 14244255014 scopus 로고    scopus 로고
    • Glucocorticoid receptor-induced MAPK phosphatase-1 (MPK-1) expression inhibits paclitaxel-associated MAPK activation and contributes to breast cancer cell survival
    • WU, W., PEW, T., ZOU, M., PANG, D. and CONZEN, S. D. (2005). Glucocorticoid receptor-induced MAPK phosphatase-1 (MPK-1) expression inhibits paclitaxel-associated MAPK activation and contributes to breast cancer cell survival. J. Biol. Chem. 280 4117-4124.
    • (2005) J. Biol. Chem , vol.280 , pp. 4117-4124
    • Wu, W.1    Pew, T.2    Zou, M.3    Pang, D.4    Conzen, S.D.5


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