Super paramagnetic Clustering of Data (SPC)

.96> i = 1; : : : ; q. Any neighboring couple, ! i; j ?, whose colors do not agree has to pay a penalty J ij that decays with distance. The cost function is defined as E (fs i g) = X !i;j? J ij \Gamma 1 \Gamma ffi s i ;s j \Delta The Maximum-Entropy principle and the average cost constraint lead to the Gibbs distribution over all possible clusterings, thus the probability for a given clustering fs i g is Prob (fs i g) = exp \GammaE (fs i g) =T Z where Z is a normalization factor and T is a Lagrange coefficient coupled to the average cost constraint. T<

Integrated Genome-wide DNA Copy Number and Expression Analysis Identifies Distinct Mechanisms of Primary Chemo-

Purpose—A significant number of women with serous ovarian cancer are intrinsically refractory to platinum-taxol based treatment. We analyzed somatic DNA copy number variation (CNV) and gene expression data to identify key mechanisms associated with primary resistance in advanced-stage serous cancers. Experimental Design—Genome-wide CNV was measured in 118 ovarian tumors using high-resolution oligonucleotide microarrays. A well-defined subset of 85 advanced-stage serous tumors was then used to relate CNV to primary resistance to treatment. The discovery-based approach was complemented by quantitative-PCR copy number analysis of twelve candidate genes as independent validation of previously reported associations with clinical outcome. Likely CNV targets and tumo