Analysis and Visualization of Gene Expression Microarray Data in Human Cancer Using Self-Organizing Maps

Authors:
Sampsa Hautaniemi;Olli Yli-Harja;Jaakko Astola;Pä/ivikki Kauraniemi;Anne Kallioniemi;Maija Wolf;Jimmy Ruiz;Spyro Mousses;Olli-P. Kallioniemi
Affiliations:
Institute of Signal Processing, Tampere University of Technology, PO Box 553, 33101 Tampere, Finland. sampsa.hautaniemi@tut.fi;Institute of Signal Processing, Tampere University of Technology, PO Box 553, 33101 Tampere, Finland. yliharja@cs.tut.fi;Institute of Signal Processing, Tampere University of Technology, PO Box 553, 33101 Tampere, Finland. jaakko.astola@tut.fi;Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, FIN-33520 Tampere, Finland. paivikki.kauraniemi@uta.fi;Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, FIN-33520 Tampere, Finland. anne.kallioniemi@uta.fi;Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, USA&semi/ Medical Biotechnology Group, VTT Technical Research Centre of Finland and University of T ...;Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, USA. jruiz@siumed.edu;Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, USA. smousses@tgen.org;Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, USA&semi/ Medical Biotechnology Group, VTT Technical Research Centre of Finland and University of T ...
Venue:
Machine Learning
Year:
2003

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Abstract

cDNA microarrays permit massively parallel gene expression analysis and have spawned a new paradigm in the study of molecular biology. One of the significant challenges in this genomic revolution is to develop sophisticated approaches to facilitate the visualization, analysis, and interpretation of the vast amounts of multi-dimensional gene expression data. We have applied self-organizing map (SOM) in order to meet these challenges. In essence, we utilize U-matrix and component planes in microarray data visualization and introduce general procedure for assessing significance for a cluster detected from U-matrix. Our case studies consist of two data sets. First, we have analyzed a data set containing 13,824 genes in 14 breast cancer cell lines. In the second case we show an example of the SOM in drug treatment of prostate cancer cells. Our results indicate that (1) SOM is capable of helping finding certain biologically meaningful clusters, (2) clustering algorithms could be used for finding a set of potential predictor genes for classification purposes, and (3) comparison and visualization of the effects of different drugs is straightforward with the SOM. In summary, the SOM provides an excellent format for visualization and analysis of gene microarray data, and is likely to facilitate extraction of biologically and medically useful information.