• DFseq: Distribution-Free Method to Detect Differential Gene Expression for RNA-Sequencing Data

    1 month ago - By IEEE/ACM

    Many current RNA-sequencing data analysis methods compare expressions one gene at a time, taking little consideration of the correlations among genes. In this study, we propose a method to convert such an one-dimensional comparison approach into a two-dimensional evaluation of the ratio of standard deviations of two constructed random variables. This method allows the identification of differentially expressed genes while controlling a preset significance level conditional on the read count mean-variance relationship. Meanwhile, correlations among genes are naturally accommodated due to...
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  • Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network

    1 month ago - By IEEE/ACM

    Accurately reconstructing gene regulatory networks from high-throughput gene expression data has been a major challenge in systems biology for decades. Many approaches have been proposed to solve this problem. However, there is still much room for the improvement of GRN inference. Integrating data from different sources is a promising strategy. Epigenetic modifications have a close relationship with gene regulation. Hence, epigenetic data such as histone modification profiles can provide useful information for uncovering regulatory interactions between genes. In this paper, we propose a...
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