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10.1073/pnas.1604351113 http://scihub22266oqcxt.onion/10.1073/pnas.1604351113 C4855614!4855614 !27078110     free     free     free Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=27078110 &cmd=llinks): Failed to open stream: HTTP request failed! 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Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system |pdf=|usr=}}{{27078110 }} gab.com Text Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system JO: Proc Natl Acad Sci U S A http://www.kidney.de/pget.php?&tw=1&pmid=27078110 #FOAvip High-throughput gene expression data are one of the primary resources for exploring complex intracellular dynamics in modern biology. The integration of large amounts of public data may allow us to examine general dynamical relationships between regulators and target genes. However, obstacles for such analyses are study-specific biases or batch effects in the original data. Here we present Immuno-Navigator, a batch-corrected gene expression and coexpression database for 24 cell types of the mouse immune system. We systematically removed batch effects from the underlying gene expression data and showed that this removal considerably improved the consistency between inferred correlations and prior knowledge. The data revealed widespread cell type-specific correlation of expression. Integrated analysis tools allow users to use this correlation of expression for the generation of hypotheses about biological networks and candidate regulators in specific cell types. We show several applications of Immuno-Navigator as examples. In one application we successfully predicted known regulators of importance in naturally occurring Treg cells from their expression correlation with a set of Treg-specific genes. For one high-scoring gene, integrin ?8 (Itgb8), we confirmed an association between Itgb8 expression in forkhead box P3 (Foxp3)-positive T cells and Treg-specific epigenetic remodeling. Our results also suggest that the regulation of Treg-specific genes within Treg cells is relatively independent of Foxp3 expression, supporting recent results pointing to a Foxp3-independent component in the development of Treg cells. Twit Text FOAVip Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system ????Proc Natl Acad Sci U S A http://www.kidney.de/pget.php?&tw=1&pmid=27078110 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=27078110 #FOAvip English Wikipedia <ref>{{Cite pmid|27078110 }}</ref> Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system #MMPMID27078110 Vandenbon A ; Dinh VH ; Mikami N ; Kitagawa Y ; Teraguchi S ; Ohkura N ; Sakaguchi S Proc Natl Acad Sci U S A 2016[Apr]; 113 (17 ): E2393-402 PMID27078110 show ga High-throughput gene expression data are one of the primary resources for exploring complex intracellular dynamics in modern biology. The integration of large amounts of public data may allow us to examine general dynamical relationships between regulators and target genes. However, obstacles for such analyses are study-specific biases or batch effects in the original data. Here we present Immuno-Navigator, a batch-corrected gene expression and coexpression database for 24 cell types of the mouse immune system. We systematically removed batch effects from the underlying gene expression data and showed that this removal considerably improved the consistency between inferred correlations and prior knowledge. The data revealed widespread cell type-specific correlation of expression. Integrated analysis tools allow users to use this correlation of expression for the generation of hypotheses about biological networks and candidate regulators in specific cell types. We show several applications of Immuno-Navigator as examples. In one application we successfully predicted known regulators of importance in naturally occurring Treg cells from their expression correlation with a set of Treg-specific genes. For one high-scoring gene, integrin ?8 (Itgb8), we confirmed an association between Itgb8 expression in forkhead box P3 (Foxp3)-positive T cells and Treg-specific epigenetic remodeling. Our results also suggest that the regulation of Treg-specific genes within Treg cells is relatively independent of Foxp3 expression, supporting recent results pointing to a Foxp3-independent component in the development of Treg cells. |*Databases, Factual [MESH] |*Gene Expression Regulation [MESH] |*Gene Regulatory Networks [MESH] |*Immune System/cytology [MESH] |*T-Lymphocytes, Regulatory [MESH] |Animals [MESH] |Forkhead Transcription Factors/genetics [MESH] |Gene Expression [MESH] |Genes, Regulator [MESH] |Genome-Wide Association Study/methods [MESH] |Hematopoiesis [MESH]Immuno-Navigator, a batch-corrected coexpression database, reveals cel(epmc).pdf DeepDyve Pubget Overpricing