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However, most of existing differential network analysis methods are designed for single-platform data analysis and assume that differences between networks are driven by individual edges.
In this study, we develop a node-based multi-view differential network analysis model to simultaneously estimate multiple gene regulatory networks and their differences from multi-platform gene expression data.
We use this transformation in our differential network analysis.
Several recent works have described differential network analysis methods for gene co-expression networks [ 11- 13].
Second, we incorporate recent developments in differential network analysis [ 22, 23].
To explicitly address differential network analysis [ 3],[ 5],[ 12], some initial efforts have been recently reported [ 1].
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These observations indicated that a differential co-expression approach could outperform the standard differential expression network analysis in searching for disease-related modules.
We propose that this differential regulation network analysis framework is feasible to gain insights into dysregulated mechanisms underlying tumorigenesis and other phenotypic changes.
To facilitate differential eigengene network analysis, we propose methods for finding consensus modules.
Here we report results of our differential eigengene network analysis of human and chimpanzee microarray brain data.
We expect the knowledge-fused differential dependency network analysis, together with the open-source R package, to be an important and useful bioinformatics tool in biological network analyses.
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