Network based consensus gene signatures for biomarker discovery in breast cancer

Diagnostic and prognostic biomarkers for cancer based on gene expression profiles are viewed as a major step towards a better personalized medicine. Many studies using various computational approaches have been published in this direction during the last decade. However, when comparing different gene signatures for related clinical questions often only a small overlap is observed. This can have various reasons, such as technical differences of platforms, differences in biological samples or their treatment in lab, or statistical reasons because of the high dimensionality of the data combined with small sample size, leading to unstable selection of genes. In conclusion retrieved gene signatures are often hard to interpret from a biological point of view. We here demonstrate that it is possible to construct a consensus signature from a set of seemingly different gene signatures by mapping them on a protein interaction network. Common upstream proteins of close gene products, which we identified via our developed algorithm, show a very clear and significant functional interpretation in terms of overrepresented KEGG pathways, disease associated genes and known drug targets. Moreover, we show that such a consensus signature can serve as prior knowledge for predictive biomarker discovery in breast cancer. Evaluation on different datasets shows that signatures derived from the consensus signature reveal a much higher stability than signatures learned from all probesets on a microarray, while at the same time being at least as predictive. Furthermore, they are clearly interpretable in terms of enriched pathways, disease associated genes and known drug targets. In summary we thus believe that network based consensus signatures are not only a way to relate seemingly different gene signatures to each other in a functional manner, but also to establish prior knowledge for highly stable and interpretable predictive biomarkers.