메뉴 건너뛰기




Volumn 12, Issue 1, 2011, Pages

Partition decoupling for multi-gene analysis of gene expression profiling data

Author keywords

[No Author keywords available]

Indexed keywords

CANCER GENE EXPRESSION; CLASSIFICATION BOUNDARY; DIFFERENTIAL EXPRESSIONS; GENE EXPRESSION MICROARRAY; GENE EXPRESSION PROFILING; STATISTICAL LEARNING TECHNIQUES; STATISTICAL PROBLEMS; UNSUPERVISED CLUSTERING;

EID: 84855175268     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-497     Document Type: Article
Times cited : (12)

References (47)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • 10.1126/science.270.5235.467, 7569999
    • Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270(5235):467-70. 10.1126/science.270.5235.467, 7569999.
    • (1995) Science , vol.270 , Issue.5235 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 3
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • 10.1073/pnas.95.25.14863, 24541, 9843981
    • Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. PNAS 1998, 95(25):14863-8. 10.1073/pnas.95.25.14863, 24541, 9843981.
    • (1998) PNAS , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 5
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • 10.1038/10343, 10391217
    • Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet 1999, 22(3):281-5. 10.1038/10343, 10391217.
    • (1999) Nat Genet , vol.22 , Issue.3 , pp. 281-285
    • Tavazoie, S.1    Hughes, J.D.2    Campbell, M.J.3    Cho, R.J.4    Church, G.M.5
  • 6
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation
    • 10.1073/pnas.96.6.2907, 15868, 10077610
    • Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. PNAS 1999, 96(6):2907-12. 10.1073/pnas.96.6.2907, 15868, 10077610.
    • (1999) PNAS , vol.96 , Issue.6 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    Kitareewan, S.5    Dmitrovsky, E.6    Lander, E.S.7    Golub, T.R.8
  • 7
    • 28644449917 scopus 로고    scopus 로고
    • How does gene expression clustering work?
    • 10.1038/nbt1205-1499, 16333293
    • D'haeseleer P. How does gene expression clustering work?. Nat Biotechnol 2005, 23(12):1499-501. 10.1038/nbt1205-1499, 16333293.
    • (2005) Nat Biotechnol , vol.23 , Issue.12 , pp. 1499-1501
    • D'haeseleer, P.1
  • 8
    • 0037342510 scopus 로고    scopus 로고
    • Comparisons and validation of statistical clustering techniques for microarray gene expression data
    • 10.1093/bioinformatics/btg025, 12611800
    • Datta S, Datta S. Comparisons and validation of statistical clustering techniques for microarray gene expression data. Bioinformatics 2003, 19(4):459-466. 10.1093/bioinformatics/btg025, 12611800.
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 459-466
    • Datta, S.1    Datta, S.2
  • 9
    • 60849101344 scopus 로고    scopus 로고
    • Clustering cancer gene expression data: a comparative study
    • 10.1186/1471-2105-9-497, 2632677, 19038021
    • De Souto M, Costa I, De Araujo D, Ludermir T, Schliep A. Clustering cancer gene expression data: a comparative study. BMC Bioinformatics 2008, 9:497. 10.1186/1471-2105-9-497, 2632677, 19038021.
    • (2008) BMC Bioinformatics , vol.9 , pp. 497
    • De Souto, M.1    Costa, I.2    De Araujo, D.3    Ludermir, T.4    Schliep, A.5
  • 11
    • 69849086336 scopus 로고    scopus 로고
    • QUBIC: a qualitative biclustering algorithm for analyses of gene expression data
    • 10.1093/nar/gkp491, 2731891, 19509312
    • Li G, Ma Q, Tang H, Paterson A, Xu Y. QUBIC: a qualitative biclustering algorithm for analyses of gene expression data. Nucleic Acids Research 2009, 37(15):e101. 10.1093/nar/gkp491, 2731891, 19509312.
    • (2009) Nucleic Acids Research , vol.37 , Issue.15
    • Li, G.1    Ma, Q.2    Tang, H.3    Paterson, A.4    Xu, Y.5
  • 12
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • 10.1016/S0092-8674(00)81683-9, 10647931
    • Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000, 100:57-70. 10.1016/S0092-8674(00)81683-9, 10647931.
    • (2000) Cell , vol.100 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 13
    • 67049159812 scopus 로고    scopus 로고
    • A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
    • 10.1371/journal.pcbi.1000382, 2671163, 19412532
    • Hudson N, Reverter A, Dalrymple B. A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol 2009, 5(5):e1000382. 10.1371/journal.pcbi.1000382, 2671163, 19412532.
    • (2009) PLoS Comput Biol , vol.5 , Issue.5
    • Hudson, N.1    Reverter, A.2    Dalrymple, B.3
  • 14
    • 58549089495 scopus 로고    scopus 로고
    • Topological structures in the equities market network
    • Leibon G, Pauls S, Rockmore D, Savell R. Topological structures in the equities market network. PNAS 2008, 105(52):20589-20594.
    • (2008) PNAS , vol.105 , Issue.52 , pp. 20589-20594
    • Leibon, G.1    Pauls, S.2    Rockmore, D.3    Savell, R.4
  • 16
    • 18744364197 scopus 로고    scopus 로고
    • Detecting clusters of different geometrical shapes in microarray gene expression data
    • 10.1093/bioinformatics/bti251, 15647300
    • Kim D, Lee K, Lee D. Detecting clusters of different geometrical shapes in microarray gene expression data. Bioinformatics 2005, 21(9):1927-1934. 10.1093/bioinformatics/bti251, 15647300.
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1927-1934
    • Kim, D.1    Lee, K.2    Lee, D.3
  • 17
    • 70349193395 scopus 로고    scopus 로고
    • Simultaneous class discovery and classification of microarray data using spectral analysis
    • 10.1089/cmb.2008.0227, 3148134, 19580522
    • Qiu P, Plevritis SK. Simultaneous class discovery and classification of microarray data using spectral analysis. J Comput Biol 2009, 16:935-944. 10.1089/cmb.2008.0227, 3148134, 19580522.
    • (2009) J Comput Biol , vol.16 , pp. 935-944
    • Qiu, P.1    Plevritis, S.K.2
  • 18
    • 2342561003 scopus 로고    scopus 로고
    • Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage
    • 10.1073/pnas.0307761101, 404097, 15096622
    • Rieger K, Hong W, Tusher V, Tang J, Tibshirani R, Chu G. Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage. PNAS 2004, 101(17):6635-6640. 10.1073/pnas.0307761101, 404097, 15096622.
    • (2004) PNAS , vol.101 , Issue.17 , pp. 6635-6640
    • Rieger, K.1    Hong, W.2    Tusher, V.3    Tang, J.4    Tibshirani, R.5    Chu, G.6
  • 22
    • 34548583274 scopus 로고    scopus 로고
    • A tutorial on spectral clustering
    • von Luxburg U. A tutorial on spectral clustering. Statistics and Computing 2007, 17(4):395-416.
    • (2007) Statistics and Computing , vol.17 , Issue.4 , pp. 395-416
    • von Luxburg, U.1
  • 23
    • 10044254422 scopus 로고    scopus 로고
    • How many clusters? An information-theoretic perspective
    • 10.1162/0899766042321751, 15516271
    • Still S, Bialek W. How many clusters? An information-theoretic perspective. Neural Computation 2004, 16(12):2483-2506. 10.1162/0899766042321751, 15516271.
    • (2004) Neural Computation , vol.16 , Issue.12 , pp. 2483-2506
    • Still, S.1    Bialek, W.2
  • 25
    • 22844453564 scopus 로고    scopus 로고
    • MCLUST: Software for model-based cluster analysis
    • Fraley C, Raftery A. MCLUST: Software for model-based cluster analysis. Journal of Classification 1999, 16(2):297-306.
    • (1999) Journal of Classification , vol.16 , Issue.2 , pp. 297-306
    • Fraley, C.1    Raftery, A.2
  • 27
  • 28
    • 34347341785 scopus 로고    scopus 로고
    • Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes
    • 10.1371/journal.pcbi.0030120, 1892608, 17571920
    • Ptitsyn AA, Zvonic S, Gimble JM. Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes. PLoS Comput Biol 2007, 3(6):e120. 10.1371/journal.pcbi.0030120, 1892608, 17571920.
    • (2007) PLoS Comput Biol , vol.3 , Issue.6
    • Ptitsyn, A.A.1    Zvonic, S.2    Gimble, J.M.3
  • 29
    • 33749999763 scopus 로고    scopus 로고
    • Group testing for pathway analysis improves comparability of different microarray datasets
    • 10.1093/bioinformatics/btl424, 16895928
    • Manoli T, Gretz N, Gröne H, Kenzelmann M, Eils R, Brors B. Group testing for pathway analysis improves comparability of different microarray datasets. Bioinformatics 2006, 22(20):2500. 10.1093/bioinformatics/btl424, 16895928.
    • (2006) Bioinformatics , vol.22 , Issue.20 , pp. 2500
    • Manoli, T.1    Gretz, N.2    Gröne, H.3    Kenzelmann, M.4    Eils, R.5    Brors, B.6
  • 30
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • 10.1073/pnas.091062498, 33173, 11309499
    • Tusher V, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. PNAS 2001, 98(9):5116. 10.1073/pnas.091062498, 33173, 11309499.
    • (2001) PNAS , vol.98 , Issue.9 , pp. 5116
    • Tusher, V.1    Tibshirani, R.2    Chu, G.3
  • 31
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
    • 10.1126/science.286.5439.531, 10521349
    • Golub T, Slonim D, Tamayo P, Huard C, Gaasenbeek M, Mesirov J, Coller H, Loh M, Downing J, Caligiuri M, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286(5439):531-537. 10.1126/science.286.5439.531, 10521349.
    • (1999) Science , vol.286 , Issue.5439 , pp. 531-537
    • Golub, T.1    Slonim, D.2    Tamayo, P.3    Huard, C.4    Gaasenbeek, M.5    Mesirov, J.6    Coller, H.7    Loh, M.8    Downing, J.9    Caligiuri, M.10
  • 33
    • 0141819106 scopus 로고    scopus 로고
    • Tissue Factor, Thrombin, and Cancer
    • Rickles F, Patierno S, Fernandez P. Tissue Factor, Thrombin, and Cancer. Chest 2003, 124(3 suppl):58S.
    • (2003) Chest , vol.124 , Issue.3 SUPPL
    • Rickles, F.1    Patierno, S.2    Fernandez, P.3
  • 34
    • 5144225237 scopus 로고    scopus 로고
    • Hepsin promotes prostate cancer progression and metastasis
    • 10.1016/j.ccr.2004.07.008, 15324701
    • Klezovitch O, Chevillet J, Mirosevich J, Roberts R, Matusik R, Vasioukhin V. Hepsin promotes prostate cancer progression and metastasis. Cancer Cell 2004, 6(2):185-195. 10.1016/j.ccr.2004.07.008, 15324701.
    • (2004) Cancer Cell , vol.6 , Issue.2 , pp. 185-195
    • Klezovitch, O.1    Chevillet, J.2    Mirosevich, J.3    Roberts, R.4    Matusik, R.5    Vasioukhin, V.6
  • 35
    • 2942598063 scopus 로고    scopus 로고
    • Cytochrome P450 gene polymorphism and cancer
    • 10.2174/1389200043335621, 15180491
    • Agúndez J. Cytochrome P450 gene polymorphism and cancer. Current Drug Metabolism 2004, 5(3):211-224. 10.2174/1389200043335621, 15180491.
    • (2004) Current Drug Metabolism , vol.5 , Issue.3 , pp. 211-224
    • Agúndez, J.1
  • 36
    • 0035953857 scopus 로고    scopus 로고
    • Genetic polymorphisms in cytochrome P450 (CYP) 1A1, CYP1A2, CYP2E1, glutathione S-transferase (GST) M1 and GSTT1 and susceptibility to prostate cancer in the Japanese population
    • 10.1016/S0304-3835(01)00398-6, 11275366
    • Murata M, Watanabe M, Yamanaka M, Kubota Y, Ito H, Nagao M, Katoh T, Kamataki T, Kawamura J, Yatani R, et al. Genetic polymorphisms in cytochrome P450 (CYP) 1A1, CYP1A2, CYP2E1, glutathione S-transferase (GST) M1 and GSTT1 and susceptibility to prostate cancer in the Japanese population. Cancer letters 2001, 165(2):171-177. 10.1016/S0304-3835(01)00398-6, 11275366.
    • (2001) Cancer letters , vol.165 , Issue.2 , pp. 171-177
    • Murata, M.1    Watanabe, M.2    Yamanaka, M.3    Kubota, Y.4    Ito, H.5    Nagao, M.6    Katoh, T.7    Kamataki, T.8    Kawamura, J.9    Yatani, R.10
  • 37
    • 23844494772 scopus 로고    scopus 로고
    • Cytochrome P450-mediated metabolism of estrogens and its regulation in human
    • 10.1016/j.canlet.2004.10.007, 16112414
    • Tsuchiya Y, Nakajima M, Yokoi T. Cytochrome P450-mediated metabolism of estrogens and its regulation in human. Cancer letters 2005, 227(2):115-124. 10.1016/j.canlet.2004.10.007, 16112414.
    • (2005) Cancer letters , vol.227 , Issue.2 , pp. 115-124
    • Tsuchiya, Y.1    Nakajima, M.2    Yokoi, T.3
  • 41
    • 77956492136 scopus 로고    scopus 로고
    • Simple and flexible classification of gene expression microarrays via Swirls and Ripples
    • 10.1186/1471-2105-11-452, 2949887, 20825641
    • Baker S. Simple and flexible classification of gene expression microarrays via Swirls and Ripples. BMC Bioinformatics 2010, 11:452. 10.1186/1471-2105-11-452, 2949887, 20825641.
    • (2010) BMC Bioinformatics , vol.11 , pp. 452
    • Baker, S.1
  • 42
    • 4344599431 scopus 로고    scopus 로고
    • Learning eigenfunctions links spectral embedding and kernel PCA
    • 10.1162/0899766041732396, 15333211
    • Bengio Y, Delalleau O, Roux N, Paiement J, Vincent P, Ouimet M. Learning eigenfunctions links spectral embedding and kernel PCA. Neural Computation 2004, 16(10):2197-2219. 10.1162/0899766041732396, 15333211.
    • (2004) Neural Computation , vol.16 , Issue.10 , pp. 2197-2219
    • Bengio, Y.1    Delalleau, O.2    Roux, N.3    Paiement, J.4    Vincent, P.5    Ouimet, M.6
  • 45
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 10.1093/bioinformatics/19.2.185, 12538238
    • Bolstad B, Irizarry R, Astrand M, Speed T. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.1    Irizarry, R.2    Astrand, M.3    Speed, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.