Neural Networks: A Comprehensive Foundation
Neural Networks: A Comprehensive Foundation
Kernel Methods for Pattern Analysis
Kernel Methods for Pattern Analysis
CLUGO: A Clustering Algorithm for Automated Functional Annotations Based on Gene Ontology
ICDM '05 Proceedings of the Fifth IEEE International Conference on Data Mining
Comparison of visualization methods for an atlas of gene expression data sets
Information Visualization
A New Metric to Measure Gene Product Similarity
BIBM '07 Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine
An introduction to kernel-based learning algorithms
IEEE Transactions on Neural Networks
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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.