Showing papers by "Chen Wang published in 2010"
TL;DR: The findings support the view that low- grade and high-grade serous carcinomas are distinctly different with low-grade, but not high- grade, serious carcinomas that are related to serous borderline tumor and cystadenoma.
52 citations
TL;DR: A new integrative strategy to combine biological knowledge and microarray data for gene ranking and uncovers novel pathway members that may shed light into the pathway deregulation in cancers.
Abstract: In cancer, gene networks and pathways often exhibit dynamic behavior, particularly during the process of carcinogenesis. Thus, it is important to prioritize those genes that are strongly associated with the functionality of a network. Traditional statistical methods are often inept to identify biologically relevant member genes, motivating researchers to incorporate biological knowledge into gene ranking methods. However, current integration strategies are often heuristic and fail to incorporate fully the true interplay between biological knowledge and gene expression data. To improve knowledge-guided gene ranking, we propose a novel method called coordinative component analysis (COCA) in this paper. COCA explicitly captures those genes within a specific biological context that are likely to be expressed in a coordinative manner. Formulated as an optimization problem to maximize the coordinative effort, COCA is designed to first extract the coordinative components based on a partial guidance from knowledge genes and then rank the genes according to their participation strengths. An embedded bootstrapping procedure is implemented to improve statistical robustness of the solutions. COCA was initially tested on simulation data and then on published gene expression microarray data to demonstrate its improved performance as compared to traditional statistical methods. Finally, the COCA approach has been applied to stem cell data to identify biologically relevant genes in signaling pathways. As a result, the COCA approach uncovers novel pathway members that may shed light into the pathway deregulation in cancers. We have developed a new integrative strategy to combine biological knowledge and microarray data for gene ranking. The method utilizes knowledge genes for a guidance to first extract coordinative components, and then rank the genes according to their contribution related to a network or pathway. The experimental results show that such a knowledge-guided strategy can provide context-specific gene ranking with an improved performance in pathway member identification.
12 citations
12 Dec 2010
TL;DR: The experimental results show that the proposed integrative scheme could construct sub-networks that are more relevant to MD than those constructed by conventional approach, and substantially improved the prediction accuracy, especially for those hard-to-classify sub-types.
Abstract: To construct biologically interpretable features and facilitate Muscular Dystrophy (MD) sub-types classification, we propose a novel integrative scheme utilizing PPI network, functional gene sets information, and mRNA profiling. The workflow of the proposed scheme includes three major steps: First, by combining protein–protein interaction network structure and gene co-expression relationship into new distance metric, we apply affinity propagation clustering to build gene sub-networks. Secondly, we further incorporate functional gene sets knowledge to complement the physical interaction information. Finally, based on constructed sub-network and gene set features, we apply multi-class support vector machine (MSVM) for MD sub-type classification, and highlight the biomarkers contributing to the sub-type prediction. The experimental results show that our scheme could construct sub-networks that are more relevant to MD than those constructed by conventional approach. Furthermore, our integrative strategy substantially improved the prediction accuracy, especially for those hard-to-classify sub-types.
3 citations