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Full-Text Articles in Genetics and Genomics
Egonet: Identification Of Human Disease Ego-Network Modules, Rendong Yang, Yun Bai, Zhaohui Qin, Tianwei Yu
Egonet: Identification Of Human Disease Ego-Network Modules, Rendong Yang, Yun Bai, Zhaohui Qin, Tianwei Yu
PCOM Scholarly Papers
Background: Mining novel biomarkers from gene expression profiles for accurate disease classification is challenging due to small sample size and high noise in gene expression measurements. Several studies have proposed integrated analyses of microarray data and protein-protein interaction (PPI) networks to find diagnostic subnetwork markers. However, the neighborhood relationship among network member genes has not been fully considered by those methods, leaving many potential gene markers unidentified. The main idea of this study is to take full advantage of the biological observation that genes associated with the same or similar diseases commonly reside in the same neighborhood of molecular networks.Results: …
Improving Gene Expression Data Interpretation By Finding Latent Factors That Co-Regulate Gene Modules With Clinical Factors, Tianwei Yu, Yun Bai
Improving Gene Expression Data Interpretation By Finding Latent Factors That Co-Regulate Gene Modules With Clinical Factors, Tianwei Yu, Yun Bai
PCOM Scholarly Papers
Background: In the analysis of high-throughput data with a clinical outcome, researchers mostly focus on genes/proteins that show first-order relations with the clinical outcome. While this approach yields biomarkers and biological mechanisms that are easily interpretable, it may miss information that is important to the understanding of disease mechanism and/or treatment response. Here we test the hypothesis that unobserved factors can be mobilized by the living system to coordinate the response to the clinical factors.Results: We developed a computational method named Guided Latent Factor Discovery (GLFD) to identify hidden factors that act in combination with the observed clinical factors to …