Discovering subgroups of patients from DNA copy number data using NMF on compacted matrices

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  De Campos, Cassio P ^a,b   Rancoita, Paola M V ^a,b,c   Kwee, Ivo ^a,b,d   Zucca, Emanuele ^e   Zaffalon, Marco ^a   Bertoni, Francesco ^b,e  

^a DALLE MOLLE INSTITUTE FOR ARTIFICIAL INTELLIGENCE IDSIA   (Switzerland)

^b INSTITUTE OF ONCOLOGY RESEARCH   (Switzerland)

^c VITA SALUTE SAN RAFFAELE UNIVERSITY   (Italy)

^d SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^e ONCOLOGY INSTITUTE OF SOUTHERN SWITZERLAND   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; CLUSTER ANALYSIS; DNA COPY NUMBER VARIATIONS; GENE EXPRESSION PROFILING; HUMANS; MODELS, THEORETICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84894283376     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0079720     Document Type: Article

References (33)

1. Maciejewski J, Tiu R, OK'eefe C (2009) Application of array-based whole genome scanning technologies as a cytogenetic tool in haematological malignancies. British Journal of Haematology 146: 479-488.
2. Lee DD, Seung HS (1999) Learning the parts of objects by non-negative matrix factorization. Nature 401: 788-791.
3. Devarajan K (2008) Nonnegative matrix factorization: An analytical and interpretive tool in computational biology. PLOS Computational Biology 4(7): e1000029.
4. Lee DD, Seung HS (2001) Algorithms for non-negative matrix factorization. In: Advances in neural information processing systems (NIPS). pp. 556-562.
5. Chigrinova E, Kwee I, Rinaldi A, Poretti G, Pruneri G, et al. (2010) Non-negative matrix factorization to perform unsupervised clustering of genome wide DNA profiles in mature B cell lymphoid neoplasms. British Journal of Haematology 150: 229-232.
6. Lee CM, Mudaliar MAV, Haggart DR, Wolf CR, Miele G, et al. (2012) Simultaneous non-negative matrix factorization for multiple large scale gene expression datasets in toxicology. PLOS ONE 7(12): e48238.
7. Schachtner R, Lutter D, Knollmüller P, Tomé AM, Theis FJ, et al. (2008) Knowledge-based gene expression classification via matrix factorization. Bioinformatics 24: 1688-1697.
8. Qi Q, Zhao Y, Li M, Simon R (2009) Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools. Bioinformatics 25: 545-547.
9. Taslaman L, Nilsson B (2012) A framework for regularized non-negative matrix factorization, with application to the analysis of gene expression data. PLOS ONE 7(11): e46331.
10. Scandurra M, Mian M, Greiner TC, Rancoita PMV, de Campos CP, et al. (2010) Genomic lesions associated with a different clinical outcome in diffuse large B-cell lymphoma treated with R-CHOP-21. British Journal of Heamatology 151: 221-231.
11. Kwee I, Capello D, Rinaldi A, Rancoita PMV, Bhagat G, et al. (2012) Genomic aberrations affecting the outcome of immunodeficiency-related diffuse large B-cell lymphoma. Leukemia & Lymphoma 53: 71-76.
12. Lenz G, Wright GW, Emre NCT, Kohlhammer H, Dave SS, et al. (2008) Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Proceedings of the National Academy of Sciences 105: 13520-13525.
13. Staaf J, Jönsson G, Ringnér M, Vallon-Christersson J, Grabau D, et al. (2010) High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer. Breast Cancer Research 12: R25.
14. Northcott P, Shih D, Peacock J, Garzia L, Morrissy A, et al. (2012) Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature 488: 49-56.
15. Vavasis SA (2009) On the complexity of nonnegative matrix factorization. SIAM Journal on Optimization 20: 1364-1377.
16. Gaussier E, Goutte C (2005) Relation between PLSA and NMF and implications. In: Proceedings of the 28th International ACM Conference on Research and Development in Information Retrieval. pp. 601-602.
17. Xu W, Liu X, Gong Y (2003) Document clustering based on non-negative matrix factorization. In: Proceedings of the 26th International ACM Conference on Research and Development in Informaion Retrieval. 267-273.
18. Corani G, de Campos CP (2011) Improving parameter learning of Bayesian networks from incomplete data. CoRR abs/1110.3239.
19. Ward Jr JH (1963) Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association 58(301): 236-244.
20. Kauffman L, Rousseeuw PJ (2005) Finding Groups in Data: An Introduction to Cluster Analysis. Wiley Series in Probability and Statistics. Wiley.
21. Simpson TI, Armstrong JD, Jarman A (2010) Merged consensus clustering to assess and improve class discovery with microarray data. BMC Bioinformatics 11: 590.
22. Davies DL, Bouldin DW (1979) A cluster separation measure. IEEE Transactions on Pattern Analysis and Machine Intelligence 1: 224-227.
23. Hubert L (1974) Approximate evaluation technique for the single-link and complete-link hierarchical clustering procedures. Journal of the American Statistical Association 69(347): 698-704.
24. Hubert LJ, Levin JR (1976) Evaluating object set partitions: Free-sort analysis and some generalizations. Journal of Verbal Learning and Verbal Behavior 15: 459-470.
25. Maimon O, Rokach L, editors (2010) Data Mining and Knowledge Discovery Handbook. Springer.
26. Rousseeuw PJ (1987) Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. Journal of Computational and Applied Mathematics 20: 53-65.
27. Rancoita PMV, Hutter M, Bertoni F, Kwee I (2009) Bayesian DNA copy number analysis. BMC Bioinformatics 10: 10.
28. Beroukhim R, Lin M, Park Y, Hao K, Zhao X, et al. (2006) Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLOS Computational Biology 2: 323-332. (Pubitemid 43794326)
29. Baudis M, Cleary ML (2001) Progenetix.net: an online repository for molecular cytogenetic aberration data. Bioinformatics 17: 1228-1229. (Pubitemid 33735351)
30. Lenz G, Staudt LM (2010) Aggressive lymphomas. New England Journal of Medicine 362(15): 1417-29.
31. Salles G, de Jong D, Xie W, Rosenwald A, Chhanabhai M, et al. (2011) Prognostic significance of immunohistochemical biomarkers in diffuse large B-cell lymphoma: a study from the Lunenburg lymphoma biomarker consortium. Blood 117: 7070-7078.
32. Hu X, Stern HM, Ge L, O'Brien C, Haydu L, et al. (2009) Genetic alterations and oncogenic pathways associated with breast cancer subtypes. Molecular Cancer Research 7: 511-522.
33. Taylor M, Northcott P, Korshunov A, Remke M, Cho Y, et al. (2012) Molecular subgroups of medulloblastoma: the current consensus. Acta Neuropathologica 123: 465-472.