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Keywords {🔍}

gesper, phenotypes, gene, sirna, article, pubmed, additional, gsps, genes, rnai, model, rsps, haystack, google, scholar, screens, file, offtarget, concordance, data, sirnas, set, pathogen, qiagen, rsa, cas, libraries, estimated, effects, phenotype, analysis, screen, target, ranked, predicted, pathways, infection, lists, enriched, methods, observed, performance, significantly, genespecific, sets, top, correlation, figure, pdf, pooled,

Topics {✒️}

}}{\mathrm{argmin}}\frac{1}{2n}{\displaystyle \sum_{ christian von mering org/packages/release/bioc/html/gesper nuclease-mediated genome editing vert}_f^2/2+\alpha {\displaystyle \sum_{ high-content image-based screens high-complexity-pooled screen analysis kinome-wide single-sirna counterpart article  google scholar target-confounded rnai screens vert}_f^2+\lambda \left[\left genome-wide single-sirna library ewa szczurek qiagen genome-wide screen rtd grants 51rt-0_126008 genome-scale rnai screen kinome-wide phenotypic readout performing inter-pathogen comparisons small-molecule knockdown experiments genome-wide qiagen screens }_j{\beta}_j+\varepsilon $$ \widehat{\beta}=\underset{\beta small interfering rna expression profiling reveals author information authors custom-rna-synthesis/sirna/ large-scale rnai screen gene-specific phenotype estimator genome-wide pooled library tgf-β signaling reveals von eichel-streiber distinct genome-wide qiagen weak seed-pairing stability kinome-wide data set established prioritization methods }{\left\vert {\beta}_j unbiased gene-level interpretation large-scale rnai screens article download pdf kinome-wide data sets pathogen infection screens image-based screens performed tenfold cross-validation deconvolution group-lasso penalty enforces pathogen-specific infection previously published screen +\varepsilon ={\displaystyle \sum_{ target-aware computational methods original author

Schema {🗺️}

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         headline:gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens
         description:Small interfering RNAs (siRNAs) exhibit strong off-target effects, which confound the gene-level interpretation of RNA interference screens and thus limit their utility for functional genomics studies. Here, we present gespeR, a statistical model for reconstructing individual, gene-specific phenotypes. Using 115,878 siRNAs, single and pooled, from three companies in three pathogen infection screens, we demonstrate that deconvolution of image-based phenotypes substantially improves the reproducibility between independent siRNA sets targeting the same genes. Genes selected and prioritized by gespeR are validated and shown to constitute biologically relevant components of pathogen entry mechanisms and TGF-β signaling. gespeR is available as a Bioconductor R-package.
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      headline:gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens
      description:Small interfering RNAs (siRNAs) exhibit strong off-target effects, which confound the gene-level interpretation of RNA interference screens and thus limit their utility for functional genomics studies. Here, we present gespeR, a statistical model for reconstructing individual, gene-specific phenotypes. Using 115,878 siRNAs, single and pooled, from three companies in three pathogen infection screens, we demonstrate that deconvolution of image-based phenotypes substantially improves the reproducibility between independent siRNA sets targeting the same genes. Genes selected and prioritized by gespeR are validated and shown to constitute biologically relevant components of pathogen entry mechanisms and TGF-β signaling. gespeR is available as a Bioconductor R-package.
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         Microbial Genetics and Genomics
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               type:PostalAddress
            type:Organization
      name:Christian von Mering
      affiliation:
            name:University of Zurich
            address:
               name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
            name:SIB Swiss Institute of Bioinformatics
            address:
               name:SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
               type:PostalAddress
            type:Organization
      name:Wolf-Dietrich Hardt
      affiliation:
            name:Department of Biology, ETH
            address:
               name:Department of Biology, ETH, Zurich, Switzerland
               type:PostalAddress
            type:Organization
      name:Christoph Dehio
      affiliation:
            name:Biozentrum, University of Basel
            address:
               name:Biozentrum, University of Basel, Basel, Switzerland
               type:PostalAddress
            type:Organization
      name:Niko Beerenwinkel
      affiliation:
            name:Department of Biosystems Science and Engineering, ETH
            address:
               name:Department of Biosystems Science and Engineering, ETH, Zurich, Switzerland
               type:PostalAddress
            type:Organization
            name:SIB Swiss Institute of Bioinformatics
            address:
               name:SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Department of Biosystems Science and Engineering, ETH, Zurich, Switzerland
      name:SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
      name:Department of Biosystems Science and Engineering, ETH, Zurich, Switzerland
      name:SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
      name:Department of Biology, ETH, Zurich, Switzerland
      name:Department of Biology, ETH, Zurich, Switzerland
      name:Department of Biology, ETH, Zurich, Switzerland
      name:Biozentrum, University of Basel, Basel, Switzerland
      name:Biozentrum, University of Basel, Basel, Switzerland
      name:Biozentrum, University of Basel, Basel, Switzerland
      name:Biozentrum, University of Basel, Basel, Switzerland
      name:Biozentrum, University of Basel, Basel, Switzerland
      name:Biozentrum, University of Basel, Basel, Switzerland
      name:Institute for Tropical Health and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
      name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
      name:SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
      name:Department of Biology, ETH, Zurich, Switzerland
      name:Biozentrum, University of Basel, Basel, Switzerland
      name:Department of Biosystems Science and Engineering, ETH, Zurich, Switzerland
      name:SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland

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