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We are analyzing https://link.springer.com/article/10.1186/1471-2164-15-1162.

Title:
Simultaneous analysis of large-scale RNAi screens for pathogen entry | BMC Genomics
Description:
Background Large-scale RNAi screening has become an important technology for identifying genes involved in biological processes of interest. However, the quality of large-scale RNAi screening is often deteriorated by off-targets effects. In order to find statistically significant effector genes for pathogen entry, we systematically analyzed entry pathways in human host cells for eight pathogens using image-based kinome-wide siRNA screens with siRNAs from three vendors. We propose a Parallel Mixed Model (PMM) approach that simultaneously analyzes several non-identical screens performed with the same RNAi libraries. Results We show that PMM gains statistical power for hit detection due to parallel screening. PMM allows incorporating siRNA weights that can be assigned according to available information on RNAi quality. Moreover, PMM is able to estimate a sharedness score that can be used to focus follow-up efforts on generic or specific gene regulators. By fitting a PMM model to our data, we found several novel hit genes for most of the pathogens studied. Conclusions Our results show parallel RNAi screening can improve the results of individual screens. This is currently particularly interesting when large-scale parallel datasets are becoming more and more publicly available. Our comprehensive siRNA dataset provides a public, freely available resource for further statistical and biological analyses in the high-content, high-throughput siRNA screening field.
Website Age:
28 years and 1 months (reg. 1997-05-29).

Matching Content Categories {📚}

  • Science
  • Education
  • Movies

Content Management System {📝}

What CMS is link.springer.com built with?

Custom-built

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Traffic Estimate {📈}

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🌠 Phenomenal Traffic: 5M - 10M visitors per month


Based on our best estimate, this website will receive around 5,000,019 visitors per month in the current month.
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How Does Link.springer.com Make Money? {💸}

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Keywords {🔍}

pubmed, screens, data, pmm, cells, pathogens, infection, gene, genes, sirna, article, pathogen, hits, google, scholar, sirnas, hit, figure, screening, pbs, analysis, rnai, cas, performed, cell, methods, parallel, set, central, number, ranking, shared, shows, results, staining, statistical, libraries, file, effects, model, min, power, monocytogenes, additional, mtt, single, image, fixed, mixed, false,

Topics {✒️}

high-throughput rnai screening large-scale rnai screening high-content rnai screening genome-scale rnai screening additional high-throughput data rna replication-center assay large-scale rnai screens numerous large-scale screens article download pdf large-scale sirna screens functional tgf-beta receptor large-scale parallel datasets infectx high-content datasets green outlines high-light linear mixed-effects models high-performance computing resources anr grant mie-2009-signrupvac open access license high-content screening serine/threonine protein kinase linear mixed model wolf-dietrich hardt immunolgie de marseille-luminy infectx data-access page ceramide-enriched membrane platforms 5 μl rnase-free ddh2o large-scale inference rnai-transfected cell plates mann–whitney-u-test host factors reveals shigella flexneri-specific protocol kinome-wide pathogen screens ordinary linear model heat map shows vaccinia virus-specific protocol full size image 𝜎 𝜖 2 bmc genomics 15 genome-wide resources salmonella typhimurium-specific protocol discover shared mechanisms raquel conde-alvarez anti-gfp antibody actin-based active part assessing differential expression hela ccl-2 cells regulates cell growth cross-validated sirna sets people cofund program access data aggregates

Schema {🗺️}

WebPage:
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         headline:Simultaneous analysis of large-scale RNAi screens for pathogen entry
         description:Large-scale RNAi screening has become an important technology for identifying genes involved in biological processes of interest. However, the quality of large-scale RNAi screening is often deteriorated by off-targets effects. In order to find statistically significant effector genes for pathogen entry, we systematically analyzed entry pathways in human host cells for eight pathogens using image-based kinome-wide siRNA screens with siRNAs from three vendors. We propose a Parallel Mixed Model (PMM) approach that simultaneously analyzes several non-identical screens performed with the same RNAi libraries. We show that PMM gains statistical power for hit detection due to parallel screening. PMM allows incorporating siRNA weights that can be assigned according to available information on RNAi quality. Moreover, PMM is able to estimate a sharedness score that can be used to focus follow-up efforts on generic or specific gene regulators. By fitting a PMM model to our data, we found several novel hit genes for most of the pathogens studied. Our results show parallel RNAi screening can improve the results of individual screens. This is currently particularly interesting when large-scale parallel datasets are becoming more and more publicly available. Our comprehensive siRNA dataset provides a public, freely available resource for further statistical and biological analyses in the high-content, high-throughput siRNA screening field.
         datePublished:2014-12-22T00:00:00Z
         dateModified:2014-12-22T00:00:00Z
         pageStart:1
         pageEnd:18
         license:https://creativecommons.org/publicdomain/zero/1.0/
         sameAs:https://doi.org/10.1186/1471-2164-15-1162
         keywords:
            High-throughput high-content RNAi screening
            Pathogen entry
            Linear mixed model
            Hit detection
            Life Sciences
            general
            Microarrays
            Proteomics
            Animal Genetics and Genomics
            Microbial Genetics and Genomics
            Plant Genetics and Genomics
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ScholarlyArticle:
      headline:Simultaneous analysis of large-scale RNAi screens for pathogen entry
      description:Large-scale RNAi screening has become an important technology for identifying genes involved in biological processes of interest. However, the quality of large-scale RNAi screening is often deteriorated by off-targets effects. In order to find statistically significant effector genes for pathogen entry, we systematically analyzed entry pathways in human host cells for eight pathogens using image-based kinome-wide siRNA screens with siRNAs from three vendors. We propose a Parallel Mixed Model (PMM) approach that simultaneously analyzes several non-identical screens performed with the same RNAi libraries. We show that PMM gains statistical power for hit detection due to parallel screening. PMM allows incorporating siRNA weights that can be assigned according to available information on RNAi quality. Moreover, PMM is able to estimate a sharedness score that can be used to focus follow-up efforts on generic or specific gene regulators. By fitting a PMM model to our data, we found several novel hit genes for most of the pathogens studied. Our results show parallel RNAi screening can improve the results of individual screens. This is currently particularly interesting when large-scale parallel datasets are becoming more and more publicly available. Our comprehensive siRNA dataset provides a public, freely available resource for further statistical and biological analyses in the high-content, high-throughput siRNA screening field.
      datePublished:2014-12-22T00:00:00Z
      dateModified:2014-12-22T00:00:00Z
      pageStart:1
      pageEnd:18
      license:https://creativecommons.org/publicdomain/zero/1.0/
      sameAs:https://doi.org/10.1186/1471-2164-15-1162
      keywords:
         High-throughput high-content RNAi screening
         Pathogen entry
         Linear mixed model
         Hit detection
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
      image:
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2164-15-1162/MediaObjects/12864_2014_Article_6988_Fig1_HTML.jpg
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         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2164-15-1162/MediaObjects/12864_2014_Article_6988_Fig3_HTML.jpg
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         volumeNumber:15
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         name:BioMed Central
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Pauli Rämö
            affiliation:
                  name:University of Basel
                  address:
                     name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Anna Drewek
            affiliation:
                  name:ETH Zurich
                  address:
                     name:Seminar for Statistics, ETH Zurich, Zurich, Switzerland
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Cécile Arrieumerlou
            affiliation:
                  name:Université Paris Descartes
                  address:
                     name:Institut Cochin, INSERM U1016, CNRS 8104, Université Paris Descartes, Paris, France
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Niko Beerenwinkel
            affiliation:
                  name:ETH Zurich
                  address:
                     name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
                     type:PostalAddress
                  type:Organization
                  name:Swiss Institute of Bioinformatics
                  address:
                     name:Swiss Institute of Bioinformatics, Basel, Switzerland
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Houchaima Ben-Tekaya
            affiliation:
                  name:University of Basel
                  address:
                     name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
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               name:Institut Pasteur, Unité des Interactions Bactéries Cellules; INSERM, U604, INRA, Paris, France
               type:PostalAddress
            type:Organization
      name:Michael Podvinec
      affiliation:
            name:University of Basel
            address:
               name:Research IT, Biozentrum, University of Basel, Basel, Switzerland
               type:PostalAddress
            type:Organization
      name:Eva Pujadas
      affiliation:
            name:University of Basel
            address:
               name:Research IT, Biozentrum, University of Basel, Basel, Switzerland
               type:PostalAddress
            type:Organization
      name:Bernd Rinn
      affiliation:
            name:ETH Zurich
            address:
               name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
            name:Swiss Institute of Bioinformatics
            address:
               name:Swiss Institute of Bioinformatics, Basel, Switzerland
               type:PostalAddress
            type:Organization
      name:Vincent Rouilly
      affiliation:
            name:University of Basel
            address:
               name:Research IT, Biozentrum, University of Basel, Basel, Switzerland
               type:PostalAddress
            type:Organization
      name:Fabian Schmich
      affiliation:
            name:ETH Zurich
            address:
               name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
      name:Juliane Siebourg-Polster
      affiliation:
            name:ETH Zurich
            address:
               name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
      name:Berend Snijder
      affiliation:
            name:University of Zurich
            address:
               name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
      name:Michael Stebler
      affiliation:
            name:ETH Zurich
            address:
               name:Light Microscopy and Screening Center, ETH Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
      name:Gabriel Studer
      affiliation:
            name:University of Basel
            address:
               name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
               type:PostalAddress
            type:Organization
      name:Ewa Szczurek
      affiliation:
            name:ETH Zurich
            address:
               name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
            name:Swiss Institute of Bioinformatics
            address:
               name:Swiss Institute of Bioinformatics, Basel, Switzerland
               type:PostalAddress
            type:Organization
      name:Matthias Truttmann
      affiliation:
            name:University of Basel
            address:
               name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
               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:Andreas Vonderheit
      affiliation:
            name:Institute of Molecular Biology
            address:
               name:Institute of Molecular Biology, Mainz, Germany
               type:PostalAddress
            type:Organization
      name:Artur Yakimovich
      affiliation:
            name:University of Zurich
            address:
               name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
      name:Peter Bühlmann
      affiliation:
            name:ETH Zurich
            address:
               name:Seminar for Statistics, ETH Zurich, Zurich, Switzerland
               type:PostalAddress
            type:Organization
      name:Christoph Dehio
      affiliation:
            name:University of Basel
            address:
               name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Seminar for Statistics, ETH Zurich, Zurich, Switzerland
      name:Institut Cochin, INSERM U1016, CNRS 8104, Université Paris Descartes, Paris, France
      name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
      name:Swiss Institute of Bioinformatics, Basel, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Institute for Tropical Health and Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
      name:Institut Pasteur, Unité des Interactions Bactéries Cellules; INSERM, U604, INRA, Paris, France
      name:Light Microscopy and Screening Center, ETH Zurich, Zurich, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
      name:Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
      name:Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Light Microscopy and Screening Center, ETH Zurich, Zurich, Switzerland
      name:Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
      name:Institut Pasteur, Unité des Interactions Bactéries Cellules; INSERM, U604, INRA, Paris, France
      name:SyBIT, SystemsX.ch, Zurich, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
      name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
      name:Institut Pasteur, Unité des Interactions Bactéries Cellules; INSERM, U604, INRA, Paris, France
      name:Research IT, Biozentrum, University of Basel, Basel, Switzerland
      name:Research IT, Biozentrum, University of Basel, Basel, Switzerland
      name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
      name:Swiss Institute of Bioinformatics, Basel, Switzerland
      name:Research IT, Biozentrum, University of Basel, Basel, Switzerland
      name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
      name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
      name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
      name:Light Microscopy and Screening Center, ETH Zurich, Zurich, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
      name:Swiss Institute of Bioinformatics, Basel, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
      name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
      name:Institute of Molecular Biology, Mainz, Germany
      name:Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
      name:Seminar for Statistics, ETH Zurich, Zurich, Switzerland
      name:Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland

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