Analysis and visualization of gene expression microarray data in human cancer using self-organizing maps

Sampsa Hautaniemi, Olli Yli-Harja, Jaakko Astola, Päivikki Kauraniemi, Anne Kallioniemi, Maija Wolf, Jimmy Ruiz, Spyro Mousses, Olli Kallioniemi

Research output: Contribution to journalArticleScientificpeer-review

38 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)45-66
JournalMachine Learning
Volume52
Issue number1-2
DOIs
Publication statusPublished - 2003
MoE publication typeA1 Journal article-refereed

Keywords

  • bioinformatics
  • gene expression
  • in human cancer
  • self-organizing map

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    Hautaniemi, S., Yli-Harja, O., Astola, J., Kauraniemi, P., Kallioniemi, A., Wolf, M., Ruiz, J., Mousses, S., & Kallioniemi, O. (2003). Analysis and visualization of gene expression microarray data in human cancer using self-organizing maps. Machine Learning, 52(1-2), 45-66. https://doi.org/10.1023/A:1023941307670