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Gastric cancer (GC) is one of the lethal cancer types as well as one of the heterogeneous cancer types. To elucidate GC molecular mechanisms, mutational co-occurrence analyses have been suggested. However, an association between mutational co-occurrences and known GC signaling contexts has yet to be identified. In this study, the known GC signaling contexts including cancer hallmarks (DNA repair,...
We performed trend analyses between the lengths of DNA copy number (CN) segments and corresponding gene expression profiles from microarray data in hepatocellular carcinoma (HCC) and colorectal carcinoma (CRC). Significant correlations were observed in CN gain of HCC and CRC (p<0.05). The trend of the CN loss showed a significant correlation in HCC whereas there was no correlation between the length...
Ovarian cancer is one of the leading causes of death in women. To describe the complex gene regulatory relationships and investigate genes acting important roles in ovarian cancer, we adopted gaussian graphic model to construct gene co-expression networks of two independent ovarian cancer datasets separately. To validate the robustness of networks, modules are identified by decision tree cut algorithm...
This study developed a method to identify disease-correlated pathways by integrating copy numbers (CN) and gene expression (GE). To evaluate the correlation between CN and GE, a suitable window size was assessed by simulation. Gene Set Enrichment Analysis (GSEA) was utilized to identify the possible pathways by CN, GE, and their correlations, respectively. Each of those enriched pathways was further...
Ovarian cancer is the leading cause of death in gynecological cancers. Carboplatinum-based therapy is the standard treatment choice for ovarian cancer. However, a majority of the patients develop resistance to carboplatinum fairly rapidly hence there is a clinical need for early predictors of carboplatinum resistance. While there are a few indicative gene markers, they have poor sensitivity and specificity...
N-(2-chloroethyl)-N′-cyclohexyl-N-nitrosoureas (CCNUs) are widely applied as antitumor agents. However, researches have indicated that their decomposition products are inclined to cause secondary cancer. Hence it is necessary to probe into both carcinogenic and anticancer mechanism of such compounds so that effective anticancer drugs with lower toxicity can be obtained. In the present work, the DFT-B3LYP...
The main novelty of this paper is to apply treelets as a feature transformation tool prior to using block diagonal linear discriminant analysis (BDLDA). Using pairwise feature transformations, treelets seek to approximate the decorrelation behavior of principal component analysis (PCA) without requiring identifying the eigenvectors of the full covariance matrix. Instead, PCA is successively applied...
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