Cancer -- Genetic aspects

Mining the human genome for therapeutic target(s) discovery promises novel outcome. Over half of the proteins in the human genome however, remain uncharacterized. These proteins offer a potential for new target(s) discovery for diverse diseases. Additional targets for cancer diagnosis and therapy are urgently needed to help move away from the cytotoxic era to a targeted therapy approach. Bioinformatics and proteomics approaches can be used to characterize novel sequences in the genome database to infer putative function. The hypothesis that the amino acid motifs and proteins domains of the uncharacterized proteins can be used as a starting point to predict putative function of these proteins provided the framework for the research discussed in this dissertation.

In recent years more and more researchers have begun to use data mining and
machine learning tools to analyze gene microarray data. In this thesis we have collected a
selection of datasets revolving around prediction of patient response in the specific area
of breast cancer treatment. The datasets collected in this paper are all obtained from gene
chips, which have become the industry standard in measurement of gene expression. In
this thesis we will discuss the methods and procedures used in the studies to analyze the
datasets and their effects on treatment prediction with a particular interest in the selection
of genes for predicting patient response. We will also analyze the datasets on our own in
a uniform manner to determine the validity of these datasets in terms of learning potential
and provide strategies for future work which explore how to best identify gene signatures.