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Kernel-based Visualisation of Genes with the Gene Ontology
Ghous, H., Kennedy, P.J., Catchpoole, D.R. and Simoff, S.J.
With the development of microarray-based high-throughput technologies for examining genetic and
biological information en masse, biologists are now
faced with making sense of large lists of genes identified from their biological experiments. There is a vital
need for "system biology" approaches which can allow
biologists to see new or unanticipated potential relationships
which will lead to new hypotheses and eventual
new knowledge. Finding and understanding relationships
in this data is a problem well suited to visualisation.
We augment genes with their associated
terms from the Gene Ontology and visualise them using
kernel Principal Component Analysis with both
specialised linear and Gaussian kernels. Our results
show that this method can correctly visualise genes
by their functional relationships and we describe the
difference between using the linear and Gaussian kernels
on the problem. |
Cite as: Ghous, H., Kennedy, P.J., Catchpoole, D.R. and Simoff, S.J. (2008). Kernel-based Visualisation of Genes with the Gene Ontology. In Proc. Seventh Australasian Data Mining Conference (AusDM 2008), Glenelg, South Australia. CRPIT, 87. Roddick, J. F., Li, J., Christen, P. and Kennedy, P. J., Eds. ACS. 133-140. |
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