  Motivation: Microarray experiments result in large scale data sets that
require extensive mining and refining to extract useful information. We have
been developing an efficient novel algorithm for nonmetric multidimensional
scaling (nMDS) analysis for very large data sets as a maximally unsupervised
data mining device. We wish to demonstrate its usefulness in the context of
bioinformatics. In our motivation is also an aim to demonstrate that
intrinsically nonlinear methods are generally advantageous in data mining.
Results: The Pearson correlation distance measure is used to indicate the
dissimilarity of the gene activities in transcriptional response of cell
cycle-synchronized human fibroblasts to serum [Iyer et al., Science vol. 283,
p83 (1999)]. These dissimilarity data have been analyzed with our nMDS
algorithm to produce an almost circular arrangement of the genes. The temporal
expression patterns of the genes rotate along this circular arrangement. If an
appropriate preparation procedure may be applied to the original data set,
linear methods such as the principal component analysis (PCA) could achieve
reasonable results, but without data preprocessing linear methods such as PCA
cannot achieve a useful picture. Furthermore, even with an appropriate data
preprocessing, the outcomes of linear procedures are not as clearcut as those
by nMDS without preprocessing.
