SiMCAL 1 algorithm for analysis of gene expression data related to the phosphatidylserine receptor
Artificial Intelligence in Medicine
ICIC'10 Proceedings of the 6th international conference on Advanced intelligent computing theories and applications: intelligent computing
High-throughput multi-dimensional scaling (HiT-MDS) for cDNA-array expression data
ICANN'05 Proceedings of the 15th international conference on Artificial Neural Networks: biological Inspirations - Volume Part I
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Motivation: Microarray experiments result in large-scale data sets that require extensive mining and refining to extract useful information. We demonstrate the usefulness of (non-metric) multidimensional scaling (MDS) method in analyzing a large number of genes. Applying MDS to the microarray data is certainly not new, but the existing works are all on small numbers ( Results: The Pearson correlation coefficient with its sign flipped is used to measure the dissimilarity of the gene activities in transcriptional response of cell-cycle-synchronized human fibroblasts to serum. These dissimilarity data have been analyzed with our nMDS algorithm to produce an almost circular relational pattern of the genes. The obtained pattern expresses a temporal order in the data in this example; the temporal expression pattern of the genes rotates along this circular arrangement and is related to the cell cycle. For the data we analyze in this paper we observe the following. If an appropriate preparation procedure is 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 clear-cut as those by nMDS without preprocessing. Availability: The FORTRAN source code of the method used in this analysis (pure nMDS) is available at http://www.granular.com/MDS/ Contact: tag@granular.com Supplementary information:http://www.granular.com/MDS/B1_2005.