Clustering of protein expression data: a benchmark of statistical and neural approaches

作者: I. H. Jarman , T. A. Etchells , D. Bacciu , J. M. Garibaldi , I. O. Ellis

DOI: 10.1007/S00500-010-0596-9

关键词:

摘要: Clustering issues are fundamental to exploratory analysis of bioinformatics data. This process may follow algorithms that reproducible but make assumptions about, for instance, the ability estimate global structure by successful local agglomeration or alternatively, they use pattern recognition methods sensitive initial conditions. paper reviews two clustering methodologies and highlights differences result from changes in data representation, applied a protein expression set breast cancer (n = 1,076). The approach model-free probabilistic competitive neural network. results compared with existing studies same set, preferred solutions profiled clinical interpretation.

参考文章(12)
H. P. Friedman, J. Rubin, On Some Invariant Criteria for Grouping Data Journal of the American Statistical Association. ,vol. 62, pp. 1159- 1178 ,(1967) , 10.1080/01621459.1967.10500923
Asa Ben-Hur, Andre Elisseeff, Isabelle Guyon, A stability based method for discovering structure in clustered data. pacific symposium on biocomputing. pp. 6- 17 ,(2001) , 10.1142/9789812799623_0002
A.R. Green, J.M. Garibaldi, D. Soria, F. Ambrogi, G. Ball, P.J.G. Lisboa, T.A. Etchells, P. Boracchi, E. Biganzoli, R.D. Macmillan, R.W. Blamey, I.O. Ellis, O-59 Identification of sub-classes of breast cancer through consensus derived from automated clustering methods Ejc Supplements. ,vol. 5, pp. 18- ,(2007) , 10.1016/S1359-6349(07)71749-4
Alfredo Vellido, Paulo J.G. Lisboa, Dolores Vicente, Robust analysis of MRS brain tumour data using t-GTM Neurocomputing. ,vol. 69, pp. 754- 768 ,(2006) , 10.1016/J.NEUCOM.2005.12.005
P.J.G. Lisboa, I.O. Ellis, A.R. Green, F. Ambrogi, M.B. Dias, Cluster-based visualisation with scatter matrices Pattern Recognition Letters. ,vol. 29, pp. 1814- 1823 ,(2008) , 10.1016/J.PATREC.2008.05.021
Dalia M. Abd El-Rehim, Graham Ball, Sarah E. Pinder, Emad Rakha, Claire Paish, John F.R. Robertson, Douglas Macmillan, Roger W. Blamey, Ian O. Ellis, High‐throughput protein expression analysis using tissue microarray technology of a large well‐characterised series identifies biologically distinct classes of breast cancer confirming recent cDNA expression analyses International Journal of Cancer. ,vol. 116, pp. 340- 350 ,(2005) , 10.1002/IJC.21004
Yvonne M Bishop, Stephen E Fienberg, Paul W Holland, None, Discrete Multivariate Analysis: Theory and Practice ,(1975)
T.A. Etchells, P.J.G. Lisboa, Orthogonal search-based rule extraction (OSRE) for trained neural networks: a practical and efficient approach IEEE Transactions on Neural Networks. ,vol. 17, pp. 374- 384 ,(2006) , 10.1109/TNN.2005.863472
Davide Bacciu, Ian H. Jarman, Terence A. Etchells, Paulo J.G. Lisboa, Patient stratification with competing risks by multivariate Fisher distance international joint conference on neural network. pp. 3453- 3460 ,(2009) , 10.1109/IJCNN.2009.5179077
Peter Langfelder, Bin Zhang, Steve Horvath, Defining clusters from a hierarchical cluster tree Bioinformatics. ,vol. 24, pp. 719- 720 ,(2008) , 10.1093/BIOINFORMATICS/BTM563