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Identification of genes and pathways involving in diseases and physiological conditions is a major task in systems biology. In this study, we develop a new non-parameter Ising model to integrate protein-protein interaction network and microarray data for identifying differentially expressed (DE) genes. We also propose a simulated annealing algorithm to find the optimal configuration of the Ising model...
Curcumin, the most active constituent of turmeric, is currently one of the major anticance new drugs and has been reported to enhance Heme Oxygenase-1(HO-1) in human brain when oxidative stress occur. Keeping the balance of HO-1 and HO-2 plays an important role in the brain. However, few researches study the effects of curcumin on the two isoenzymes of HO. Here we investigated the effects of curcumin...
Vascular endothelial growth factor (VEGF) has been shown to increase the adhesion of human breast cancer cells to human brain endothelium [1]. However, how VEGF accomplishes this is not well understood. We hypothesize that VEGF compromises the integrity of brain microvascular endothelium is one mechanism to increase the tumor cell adhesion. To test our hypothesis, using a Transwell system, we measured...
Gene expression patterns that can distinguish to a clinically significant degree disease subclasses not only play a prominent role in diagnosis but also lead to therapeutic strategies that tailor treatment to the particular biology of each disease. Nevertheless, gene expression signatures derived through statistical feature identification procedures on population datasets have received rightful criticism,...
Cancer cells exhibit a common phenotype of uncontrolled cell growth, but this phenotype may arise from many different combinations of mutations. By inferring how cells evolve in individual tumors, a process called cancer progression, we may be able to identify important mutational events for different tumor types, potentially leading to new therapeutics and diagnostics. Prior work has shown that it...
The aim of this study is to identify a gene expression signature which is characteristic of ER status in breast cancer patients. To our knowledge, this is the first microarray study in Greece involving clinical samples. We identified 97 genes that are characteristic for ER status and can well distinguish the ER+ from the ER- samples. We shrank our list to a 11-gene list correlating to the same patient...
We characterize three small gene signatures derived consequently from the original 232-gene breast cancer aggressiveness signature which could improve biological classification and clinical assignment of ~50% of breast cancer patients having histologic grade 2 tumors . Here, we develop a novel approach to identify small gene signatures providing statistically reliable, biological important and clinical...
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