Integrated analysis of gene expression and copy number data on gene shaving using independent component analysis

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 8, Issue 6, 2011, Pages 1568-1579

  Sheng, Jinhua ^a   Deng, Hong Wen ^b   Calhoun, Vince ^c   Wang, Yu Ping ^d,e  

^a INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b TULANE UNIVERSITY   (United States)

^c MIND RESEARCH NETWORK   (United States)

^d Tulane University   (United States)

^e SHANGHAI UNIVERSITY   (China)

Author keywords

Clustering technique; comparative genomic hybridization (CGH); copy number variation (CNV); gene expression; gene shaving; generalized singular value decomposition (GSVD); Independent component analysis (ICA)

Indexed keywords

CLUSTERING TECHNIQUES; COMPARATIVE GENOMIC HYBRIDIZATIONS; COPY NUMBER VARIATION (CNV); GENERALIZED SINGULAR VALUE DECOMPOSITION; INDEPENDENT COMPONENTS;

DISEASES; INDEPENDENT COMPONENT ANALYSIS; SINGULAR VALUE DECOMPOSITION;

GENE EXPRESSION;

ARTICLE; BREAST TUMOR; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; FEMALE; GENE DOSAGE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; HUMAN; METHODOLOGY;

BREAST NEOPLASMS; COMPARATIVE GENOMIC HYBRIDIZATION; DATABASES, GENETIC; FEMALE; GENE DOSAGE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 80052914729     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.71     Document Type: Article

References (42)

1. Int'l Human Genome Sequencing Consortium, "Finishing the Euchromatic Sequence of the Human Genome," Nature, vol. 431, pp. 931-945, Oct. 2004.
2. D.J. Lockhart, H. Dong, M.C. Byrne, M.T. Follettie, M.V. Gallo, M.S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E.L. Brown, "Expression Monitoring by Hybridization to High-Density Oligonucleotide Arrays," Nature Biotechnology, vol. 14, pp. 1675-1680, Dec. 1996. (Pubitemid 26414810)
3. M. Schena, D. Shalon, R.W. Davis, and P.O. Brown, "Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray," Science, vol. 270, pp. 467-470, Oct. 1995.
4. G.B. Bezerra, G.M.A. Cançado, M. Menossi, L.N. de Castro, and F.J. Von Zuben, "Recent Advances in Gene Expression Data Clustering: A Case Study with Comparative Results," Genetics and Molecular Research, vol. 4, pp. 514-524, 2005.
5. J. Chen and Y.-P. Wang, "A Statistical Model-Based Approach for the Identification of DNA Copy Number Changes in Array CGH Data Sets," IEEE/ACM Trans. Computational Biology and Bioinfor-matics, vol. 6, no. 4, pp. 529-541, Oct.-Dec. 2009.
6. S.L. Pomeroy, P. Tamayo, M. Gaasenbeek, L.M. Sturla, M. Angelo, M.E. McLaughlin, J.Y.H. Kim, L.C. Goumnerova, P.M. Black, C. Lau, J.C. Allen, D. Zagzag, J.M. Olson, T. Curran, C. Wetmore, J.A. Biegel, T. Poggio, S. Mukherjee, R. Rifkin, A. Califano, G. Stolovitzky, D.N. Louis, J.P. Mesirov, E.S. Lander, and T.R. Golub, "Prediction of Central Nervous System Embryonal Tumor Outcome Based on Gene Expression," Nature, vol. 41, pp. 436-442, 2002. (Pubitemid 34100955)
7. O.P. Kallioniemi, A. Kallioniemi, J. Piper, J. Isola, F.M. Waldman, J.W. Gray, and D. Pinkel, "Optimizing Comparative Genomic Hybridization for Analysis of DNA Sequence Copy Number Changes in Solid Tumors," Genes Chromosomes Cancer, vol. 10, pp. 231-243, 1994. (Pubitemid 24238430)
8. A. Kallioniemi, "CGH Microarrays and Cancer," Current Opinion in Biotechnology, vol. 19, pp. 36-40, 2008.
9. M. Shinawi, S.W. Cheung, "The Array CGH and Its Clinical Applications," Drug Discovery Today, vol. 13, pp. 760-770, 2008.
10. M.R. Speicher and N.P. Carter, "The New Cytogenetics: Blurring the Boundaries with Molecular Biology," Nature Reviews Genetics, vol. 6, pp. 782-792, 2005. (Pubitemid 41400836)
11. H. Lee, S.W. Kong, and P.J. Park, "Integrative Analysis Reveals the Direct and Indirect Interactions between DNA Copy Number Aberrations and Gene Expression Changes," Bioinformatics, vol. 24, pp. 889-896, 2008. (Pubitemid 351448021)
12. R.X. Menezes, M. Boetzer, M. Sieswerda, G.B. Ommen, and J.M. Boer, "Integrated Analysis of DNA Copy Number and Gene Expression Microarray Data Using Gene Sets," BMC Bioinfor-matics, vol. 10, pp. 203-217, 2009.
13. M. Schäfer, H. Schwender, S. Merk, C. Haferlach, K. Ickstadt, and M. Dugas, "Integrated Analysis of Copy Number Alterations and Gene Expression: A Bivariate Assessment of Equally Directed Abnormalities," Bioinformatics, vol. 25, pp. 3228-3235, 2009.
14. C. Soneson, H. Lilljebjörn, T. Fioretos, and M. Fontes, "Integrative Analysis of Gene Expression and Copy Number Alterations Using Canonical Correlation Analysis," BMC Bioinformatics, vol. 11, pp. 191-211, 2010.
15. E. Hyman, P. Kauraniemi, S. Hautaniemi, M. Wolf, S. Mousses, E. Rozenblum, M. Ringneár, G. Sauter, O. Monni, A. Elkahloun, O.P. Kallioniemi, and A. Kallioniemi, "Impact of DNA Amplification on Gene Expression Patterns in Breast Cancer," Cancer Research, vol. 62, pp. 6240-6245, 2002. (Pubitemid 35244477)
16. J.R. Pollack, T. Sørlie, C.M. Perou, C.A. Rees, S.S. Jeffrey, P.E. Lonning, R. Tibshirani, D. Botstein, A.L. Børresen-Dale, and P.O. Brown, "Microarray Analysis Reveals a Major Direct Role of DNA Copy Number Alteration in the Transcriptional Program of Human Breast Tumors," Proc. Nat'l Academy of Sciences USA, vol. 99, pp. 12963-12968, 2002.
17. A.J. Aguirre, C. Brennan, G. Bailey, R. Sinha, B. Feng, C. Leo, Y. Zhang, J. Zhang, J.D. Gans, N. Bardeesy, C. Cauwels, C. Cordon-Cardo, M.S. Redston, R.A. DePinho, and L. Chin, "High-Resolution Characterization of the Pancreatic Adenocarcinoma Genome," Proc. Nat'l Academy of Sciences USA, vol. 101, pp. 9067-9072, 2004. (Pubitemid 38781612)
18. D. Tsafrir, M. Bacolod, Z. Selvanayagam, I. Tsafrir, J. Shia, Z. Zeng, H. Liu, C. Krier, R.F. Stengel, F. Barany, W.L. Gerald, P.B. Paty, E. Domany, and D.A. Notterman, "Relationship of Gene Expression and Chromosomal Abnormalities in Colorectal Cancer," Cancer Research, vol. 66, pp. 2129-2137, 2006.
19. J.L. Phillips, S.W. Hayward, Y. Wang, J. Vasselli, C. Pavlovich, H. Padilla-Nash, J.R. Pezullo, B.M. Ghadimi, G.D. Grossfeld, A. Rivera, W.M. Linehan, G.R. Cunha, and T. Ried, "The Consequences of Chromosomal Aneuploidy on Gene Expression Profiles in a Cell Line Model for Prostate Carcinogenesis," Cancer Research, vol. 61, pp. 8143-8149, 2001. (Pubitemid 33091605)
20. G. Tonon, K.K. Wong, G. Maulik, C. Brennan, B. Feng, Y. Zhang, D.B. Khatry, A. Protopopov, M.J. You, A.J. Aguirre, E.S. Martin, Z. Yang, H. Ji, L. Chin, and R.A. DePinho, "High-Resolution Genomic Profiles of Human Lung Cancer," Proc. Nat'l Academy of Sciences USA, vol. 102, pp. 9625-9630, 2005. (Pubitemid 40981731)
21. R. Mao, X. Wang, E.L. Spitznagel, L.P. Frelin, J.C. Ting, H. Ding, J.W. Kim, I. Ruczinski, T.J. Downey, and J. Pevsner, "Primary and Secondary Transcriptional Effects in the Developing Human Down Syndrome Brain and Heart," Genome Biology, vol. 6, pp. R107.1-R107.20, 2005.
22. K.J. Bussey, K. Chin, S. Lababidi, M. Reimers, W.C. Reinhold, W.L. Kuo, F. Gwadry, Ajay, H. Kouros-Mehr, J. Fridlyand, A. Jain, C. Collins, S. Nishizuka, G. Tonon, A. Roschke, K. Gehlhaus, I. Kirsch, D.A. Scudiero, J.W. Gray, and J.N. Weinstein, "Integration Data on DNA Copy Number with Gene Expression Levels and Drug Sensitivities in the NCI-60 Cell Line Panel," Molecular Cancer Therapeutics, vol. 5, pp. 853-867, 2006. (Pubitemid 43724584)
23. W.N. van Wieringen and M.A. van de Wiel, "Nonparametric Testing for DNA Copy Number Induced Differential mRNA Gene Expression," Biometrics, vol. 65, pp. 19-29, 2009.
24. K. Chin, S.D. Vries, J. Fridlyand, P.T. Spellman, R. Roydasgupta, W.-L. Kuo, A. Lapuk, R.M. Neve, Z. Qian, T. Ryder, F. Chen, H. Feiler, T. Tokuyasu, C. Kingsley, S. Dairkee, Z. Meng, K. Chew, D. Pinkel, A. Jain, B.M. Ljung, L. Esserman, D.G. Albertson, F.M. Waldman, and J.W. Gray, "Genomic and Transcriptional Aberrations Linked to Breast Cancer Pathophysiologies," Cancer Cell, vol. 10, pp. 529-41, 2006. (Pubitemid 44854748)
25. H.M. Horlings, C. Lai, D.S.A. Nuyten, H. Halfwerk, P. Kristel, E. Beers, S.A. Joosse, C. Klijn, P.M. Nederlof, M.J.T. Reinders, L.F.A. Wessels, and M.J. Vijver, "Integration of DNA Copy Number Alterations and Prognostic Gene Expression Signatures in Breast Cancer Patients," Clinical Cancer Research, vol. 16, pp. 651-663, 2010.
26. O. Alter, P.O. Brown, and D. Botstein, "Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling," Proc. Nat'l Academy of Sciences USA, vol. 97, pp. 10101-10106, Aug. 2000.
27. T. Hastie, R. Tibshirani, M.B. Eisen, A. Alizadeh, R. Levy, L. Staudt, W.C. Chan, D. Botstein, and P. Brown, "'Gene Shaving' as a Method for Identifying Distinct Sets of Genes with Similar Expression Patterns," Genome Biology, vol. 1, no. 3, pp. 1-20, 2000.
28. J.A. Berger, S. Hautaniemi, S.K. Mitra, and J. Astola, "Jointly Analyzing Genes Expression and Copy Number Data in Breast Cancer Using Data Reduction models," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 1, pp. 2-16, Jan.-Mar. 2006. (Pubitemid 43269823)
29. V. Calhoun, J. Liu, and T. Adali, "A Review of Group ICA for fMRI Data and ICA for Joint Inference of Imaging, Genetic, and ERP Data," NeuroImage, vol. 45, pp. S163-S172, 2009.
30. V.D. Calhoun, T. Adali, G.D. Pearlson, and K.A. Kiehl, "Neuronal Chronometry of Target Detection Fusion of Hemodynamic and Event-Related Potential Data," NeuroImage, vol. 30, pp. 544-553, 2006.
31. Y.-P. Wang, "Integration of Gene Expression and Gene Copy Number Variations with Independent Component Analysis," Proc. IEEE Int'l Conf. Eng. Medicine and Biology Soc. (EMBS), pp. 5700-5703, 2008.
32. W. Liebermeister, "Linear Modes of Gene Expression Determined by Independent Component Analysis," Bioinformatics, vol. 18, pp. 51-60, 2002. (Pubitemid 34145031)
33. A. Hyvärinen, "Independent Component Analysis: Algorithms and Applications," Neural Networks, vol. 13, nos. 4/5, pp. 411-430, 2000. (Pubitemid 30447427)
34. A.J. Bell and T.J. Sejnowski, "An Information Maximization Approach to Blind Separation and Blind Deconvolution," Neural Computation, vol. 7, no. 6, pp. 1129-1159, 1995.
35. A. Hyvärinen and E. Oja, "A Fast Fixed-Point Algorithm for Independent Component Analysis," Neural Computation, vol. 9, no. 7, pp. 1483-1492, 1997. (Pubitemid 127462801)
36. J.F. Cardoso and A. Souloumiac, "Blind Beamforming for Non-Gaussian Signals," IEE Proc.-F, vol. 140, no. 6, pp. 362-370, 1993.
37. J. Sheng, H.-W. Deng, V. Calhoun, and Y.-P. Wang, "Webpage: Integrated Analysis of Gene Expression and Copy Number Data on Gene Shaving Using Independent Component Analysis," http://sites.google.com/site/ geneticimaging/file-cabinet, 2011.
38. P. Wang, Y. Kim, J. Pollack, B. Narasimhan, and R. Tibshirani, "A Method for Calling Gains and Losses in Array CGH Data," Biostatistics, vol. 6, pp. 45-58, Jan. 2005. (Pubitemid 41240369)
39. S. Attoor, E.R. Dougherty, Y. Chen, M.L. Bittner, and J.M. Trent, "Which is Better for cDNA-Microarray-Based Classification: Ratios or Direct Intensities," Bioinformatics, vol. 20, pp. 2513-2520, Nov. 2004. (Pubitemid 39530137)
40. O. Monni, M. Bärlund, S. Mousses, J. Kononen, G. Sauter, M. Heiskanen, P. Paavola, K. Avela, Y. Chen, M.L. Bittner, and A. Kallioniemi, "Comprehensive Copy Number and Gene Expression Profiling of the 17q23 Amplicon in Human Breast Cancer," Proc. Nat'l Academy of Sciences USA, vol. 98, pp. 5711-5716, May. 2001. (Pubitemid 32435707)
41. P. Kauraniemi, S. Hautaniemi, R. Autio, J. Astola, O. Monni, A. Elkahloun, A. Kallioniemi, "Effects of Herceptin Treatment on Global Gene Expression Patterns in HER2-Amplified and Non-Amplified Breast Cancer Cell Lines," Oncogene, vol. 23, pp. 1010-1013, Jan. 2004. (Pubitemid 38250948)
42. J.R. Pollack, T. Sørlie, C.M. Perou, C.A. Rees, S.S. Jeffrey, P.E. Lonning, R. Tibshirani, D. Botstein, A.L. Børresen-Dale, and P.O. Brown, "Microarray Analysis Reveals a Major Direct Role of DNA Copy Number Alteration in the Transcriptional Program of Human Breast Tumors," Proc. Nat'l Academy of Sciences USA, vol. 99, pp. 12963-12968, 2002.