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Single-Cell Gene Expression Profiles for Classification Problems

Gualandi, Stefano; Codegoni, Andrea; Vercesi, Eleonora


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{
  "description": "<p>This repository contains a collection of three datasets we use to introduce the Gene Mover Distance in [1] and described below. The three datasets are exported with a basic text-based format (.csv file) like other public datasets largely used in the Machine Learning community.</p>\n\n<p>The three datasets are extracted from the Gene Expression Omnibus (GEO) database [2], where they appear, respectively,&nbsp;with access number&nbsp;GSE116256 (blood leukemia, [3]), GSE84133 (human pancreas, [4]), and GSE67835 (human brain, [5]). In GEO, the datasets are decomposed into several files, which contain much more details than those reported in this version.</p>\n\n<p>However, the proposed format should facilitate other researchers in using this data.</p>\n\n<p>The Gene Mover&#39;s Distance is a measure of similarity between a pair of cells based on their gene expression profiles obtained via single-cell RNA sequencing. The underlying idea of GMD is to interpret the gene expression array of a single cell as a discrete probability measure. The distance between two cells is hence computed by solving an Optimal Transport problem between the two corresponding discrete measures. The Gene Mover&#39;s Distance can be used, for instance, to solve two classification problems: the classification of cells according to their condition and according to their type.</p>\n\n<p>The repository contains a python script to check the basic statistics of the data.</p>\n\n<p>&nbsp;</p>\n\n<p>[1] Bellazzi, R., Codegoni, A., Gualandi, S., Nicora, G., Vercesi, E. <em>The Gene Mover&#39;s Distance: Single-cell similarity via Optimal Transport</em>. <a href=\"https://arxiv.org/abs/2102.01218\">https://arxiv.org/abs/2102.01218</a></p>\n\n<p>[2] Gene Expression Omnibus (GEO) database, <a href=\"http://www.ncbi.nlm.nih.gov/geo\">http://www.ncbi.nlm.nih.gov/geo</a></p>\n\n<p>[3] van Galen, P., Hovestadt, V., Wadsworth II, M.H., Hughes, T.K., Griffin, G.K., Battaglia, S., Verga, J.A., Stephansky, J., Pastika, T.J., Story, J.L. and Pinkus, G.S., 2019. <em>Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity</em>. Cell, 176(6), pp.1265-1281.</p>\n\n<p>[4] Baron, M., Veres, A., Wolock, S.L., Faust, A.L., Gaujoux, R., Vetere, A., Ryu, J.H., Wagner, B.K., Shen-Orr, S.S., Klein, A.M. and Melton, D.A., 2016.<em> A single-cell transcriptomic map of the human and mouse pancreas reveals inter-and intra-cell population structure</em>. Cell systems, 3(4), pp.346-360.</p>\n\n<p>[5] Darmanis, S., Sloan, S.A., Zhang, Y., Enge, M., Caneda, C., Shuer, L.M., Gephart, M.G.H., Barres, B.A. and Quake, S.R., 2015. <em>A survey of human brain transcriptome diversity at the single cell level</em>. Proceedings of the National Academy of Sciences, 112(23), pp.7285-7290.</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "University of Pavia", 
      "@id": "https://orcid.org/0000-0002-2111-3528", 
      "@type": "Person", 
      "name": "Gualandi, Stefano"
    }, 
    {
      "affiliation": "University of Pavia", 
      "@type": "Person", 
      "name": "Codegoni, Andrea"
    }, 
    {
      "affiliation": "University of Pavia", 
      "@type": "Person", 
      "name": "Vercesi, Eleonora"
    }
  ], 
  "url": "https://zenodo.org/record/4604569", 
  "datePublished": "2021-03-15", 
  "version": "v1.0.0", 
  "keywords": [
    "Gene-expression-profile, Leukemia, Brain, Pancreas, Gene Mover Distance"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/c0b51f22-9ef2-4736-8348-4531c1abe1bc/gmd_v1.0.0.zip", 
      "encodingFormat": "zip", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.4604569", 
  "@id": "https://doi.org/10.5281/zenodo.4604569", 
  "@type": "Dataset", 
  "name": "Single-Cell Gene Expression Profiles for Classification Problems"
}
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