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  "Title": "Inferring tumor-specific cancer dependencies through integrating\nex-vivo drug response assays and drug-protein profiling",
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  "Authors@R": "c(person(given = \"Junyan\",\nfamily = \"Lu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jylu1118@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9211-0746\")),\nperson(given = \"Alina\",\nfamily = \"Batzilla\",\nrole = c(\"aut\")))",
  "Description": "DepInfeR integrates two experimentally accessible input\ndata matrices: the drug sensitivity profiles of cancer cell\nlines or primary tumors ex-vivo (X), and the drug affinities of\na set of proteins (Y), to infer a matrix of molecular protein\ndependencies of the cancers (ß). DepInfeR deconvolutes the\nprotein inhibition effect on the viability phenotype by using\nregularized multivariate linear regression. It assigns a\n“dependence coefficient” to each protein and each sample, and\ntherefore could be used to gain a causal and accurate\nunderstanding of functional consequences of genomic aberrations\nin a heterogeneous disease, as well as to guide the choice of\npharmacological intervention for a specific cancer type,\nsub-type, or an individual patient. For more information,\nplease read out preprint on bioRxiv:\nhttps://doi.org/10.1101/2022.01.11.475864.",
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      "title": "Use DepInfeR package to infer sample-specific protein dependencies from drug-protein profiling and ex-vivo drug response data",
      "author": "Alina Batzilla, Junyan Lu",
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        "Data input",
        "Pre-processing the drug-protein dataset",
        "Preparation of the drug response matrix",
        "Prepare drug response matrix using z-scores",
        "Assessment of missing values",
        "Subset for cell lines with less than 24 missing values (based on assessment above)",
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        "Combine the feature and response matrix for the regression model",
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        "Heatmap of protein dependence coefficients",
        "Differential dependence on proteins associated with cancer types and genotypes",
        "Visualize protein associations with cancer type",
        "Visualize P-values of significant associations between protein dependence and mutational background",
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      "modified": "2022-04-05 18:36:26",
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