232 research outputs found

    A statistical normalization method and differential expression analysis for RNA-seq data between different species

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    Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved transcriptional responses. To remove systematic variation between different species for a fair comparison, the normalization procedure serves as a crucial pre-processing step that adjusts for the varying sample sequencing depths and other confounding technical effects. Results: In this paper, we propose a scale based normalization (SCBN) method by taking into account the available knowledge of conserved orthologous genes and hypothesis testing framework. Considering the different gene lengths and unmapped genes between different species, we formulate the problem from the perspective of hypothesis testing and search for the optimal scaling factor that minimizes the deviation between the empirical and nominal type I errors. Conclusions: Simulation studies show that the proposed method performs significantly better than the existing competitor in a wide range of settings. An RNA-seq dataset of different species is also analyzed and it coincides with the conclusion that the proposed method outperforms the existing method. For practical applications, we have also developed an R package named "SCBN" and the software is available at http://www.bioconductor.org/packages/devel/bioc/html/SCBN.html

    Municipal Government Use of Social Media: An Analysis of Three Chinese Cities

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    To investigate the use of information dissemination and public communication by Chinese municipal governments, we analyzed the social media use of three large cities with relatively mature social media development: Shanghai, Nanjing and Chengdu. We collected 4,429 government posts and users’ likes, shares and comments from Weibo accounts of each city’s information office. Government posts were coded into 7 types and 16 topics. We used cross-tabulation, correlation analysis and multivariate linear regression to analyze government posts, user responses and their inter-relationships. Chengdu has issued the most posts, while Nanjing has received the highest average user response to posts and exhibited the best signs of success in communication between the government and citizens
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