Commit 4ea37f04 authored by Cosmin  SAVEANU's avatar Cosmin SAVEANU
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<title>Genetic interaction mapping (GIM) companion site</title>
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<h4>Companion web interface for the data described in the article:</h4>
<h3>Genetic interaction profiles predict links between mRNA translation and degradation factors in yeast</h3>
<p>Laurence Decourty<sup>1</sup>, Christophe Malabat<sup>2</sup>, Emmanuel Frachon<sup>3</sup>, Alain Jacquier<sup>1</sup>, Cosmin Saveanu<sup>1*</sup>
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<p><b>1</b> – Génétique des Interactions Macromoléculaires, Genomes and Genetics Department, Institut Pasteur, 25-28 rue du docteur Roux 75015 Paris, France; <b>2</b> – Hub Bioinformatique et Biostatistique, Institut Pasteur, 25-28 rue du docteur Roux 75015 Paris, France; <b>3</b> – Plate-forme Technologique Biomatériaux et Microfluidique, Institut Pasteur, 25-28 rue du docteur Roux 75015 Paris, France</p>
<h4>Abstract</h4>
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Individual mutations in yeast can be combined in a single cell and the effect on growth measured on a large scale using Genetic Interactions Mapping, or GIM (Decourty et al., PNAS 2008). We performed and analyzed the results of combining 154 mutants in yeast genes with about 5000 other mutants to identify new factors affecting RNA metabolism. To confirm the utility of our large scale results, we assigned and validated a link between inositol phosphate metabolism and translation initiation via the export of the initiation tRNA. These results, when combined with previous data sets, constitute a resource of high confidence genetic interactions in <i>S. cerevisiae</i>.
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<h3>Using the application</h3>
<p>There are two types of information on display in this application, selectable with the upper tab titles. The first, called <b>"Screens comparison"</b> correspond to looking at screens results by selecting two of interest. The screns to be compared are selected (typing part of the gene name works) and the comparison of the corrected log2(query/reference) values is displayed in a scatter plot.</p>
<p>The labels of mutants for which values are lower or higher than a pre-defined threshold are shown on the graph. Clicking and brushing allows the selection of a region of the plot. The values in that region are displayed in the data table at the bottom of the page. The data table can be scrolled to see all the screens, filtered by screen or value and ordered by clicking on the header
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The second type of information that can be explored is to be found under the <b>"Mutant profiles"</b> title. Selecting a mutant of interest leads to a display of a table of log2(Q/R) values for that mutant in the 154 screens (left side). On the right side of the page a table of 100 other mutants that had similar GIM profiles, together with the Pearson correlation coefficient are displayed. All the tables can be ordered by any column or filtered.
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<h4>Contact and further information</h4>
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Our <a href="https://research.pasteur.fr/en/team/group-cosmin-saveanu/">group page</a> and <a href="https://research.pasteur.fr/en/team/gim/">laboratory page</a>.
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Made with <a href="https://shiny.rstudio.com/">Shiny</a> and <a href="https://cran.r-project.org/">R</a>.
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