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Diagnostic breast cancer tests based on expression are already being offered commercially, although it is unclear which specific sets are superior, due to minimal gene overlap between predictive sets.
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The same clustering of samples based on expression was observed using principle component analysis and explained the majority of the variation observed in the data set (data not shown).
From this set, we found that 2.5 to 5.8% and 0.5 to 12.5% of genes called as biased based on expression were called methylated by our criteria at promoters or gene bodies, respectively.
Building classifiers based on expression profiles is an active field of research, but little attention has been paid yet to genome-based classification.
Models based on gene expression are compared with models based on clinical information to evaluate the gain in predictive accuracy over standard clinical management parameters.
Tests based on expression indices were carried out on the RMA probe set summary values.
To prevent ascertainment bias, GO annotation solely based on expression evidence was excluded.
To visualise the relationships between samples, a second dendrogram based on expression profiles is shown on the top.
An adjacency matrix based on expression correlation was created using a soft threshold procedure to allow a scale free topology.
With advances in genome-wide gene expression technologies, classification of cancer subtypes based on expression signatures is widespread and results in many biomarkers for various cancers.
Using this approach we analysed if gene's assignment to the Early, Middle or Late group based on expression pattern is connected with special features in promoter structure.
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