Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks

<p>Abstract</p> <p>Background</p> <p>Transcriptional regulation by transcription factor (TF) controls the time and abundance of mRNA transcription. Due to the limitation of current proteomics technologies, large scale measurements of protein level activities of TFs is usually infeasible, making computational reconstruction of transcriptional regulatory network a difficult task.</p> <p>Results</p> <p>We proposed here a novel Bayesian non-negative factor model for TF mediated regulatory networks. Particularly, the non-negative TF activities and sample clustering effect are modeled as the factors from a Dirichlet process mixture of rectified Gaussian distributions, and the sparse regulatory coefficients are modeled as the loadings from a sparse distribution that constrains its sparsity using knowledge from database; meantime, a Gibbs sampling solution was developed to infer the underlying network structure and the unknown TF activities simultaneously. The developed approach has been applied to simulated system and breast cancer gene expression data. Result shows that, the proposed method was able to systematically uncover TF mediated transcriptional regulatory network structure, the regulatory coefficients, the TF protein level activities and the sample clustering effect. The regulation target prediction result is highly coordinated with the prior knowledge, and sample clustering result shows superior performance over previous molecular based clustering method.</p> <p>Conclusions</p> <p>The results demonstrated the validity and effectiveness of the proposed approach in reconstructing transcriptional networks mediated by TFs through simulated systems and real data.</p

Multidimensional sound propagation in 3D high-order topological sonic insulator

High-order topological insulators (TIs) develop the conventional bulk-boundary correspondence theory and rise the interest in searching innovative topological materials. To realize a high-order TI with a wide passband of 1D and 2D transportation modes, we design non-trivial and trivial 3D sonic crystals whose combination mimics the Su-Schrieffer-Heeger model. The high-order topological boundary states can be found at the interfaces, including 0D corner state, 1D hinge state, and 2D surface state. The fabricated sample with the bent two-dimensional and one-dimensional acoustic channels exhibits the multidimensional sound propagation in space, and also verifies the transition between the complete band gap, hinge states, and surface states within the bulk band gap. Among them, the bandwidth of the single-mode hinge state achieves a large relative bandwidth 9.1%, in which sound transports one-dimensionally without significant leak into the surfaces or the bulk. The high-order topological states in the study pave the way for multidimensional sound manipulation in space.Comment: 21 pages, 7 figure