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Single-Cell Gene Expression Profiles for Classification Problems

Gualandi, Stefano; Codegoni, Andrea; Vercesi, Eleonora


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  <identifier identifierType="DOI">10.5281/zenodo.4604569</identifier>
  <creators>
    <creator>
      <creatorName>Gualandi, Stefano</creatorName>
      <givenName>Stefano</givenName>
      <familyName>Gualandi</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2111-3528</nameIdentifier>
      <affiliation>University of Pavia</affiliation>
    </creator>
    <creator>
      <creatorName>Codegoni, Andrea</creatorName>
      <givenName>Andrea</givenName>
      <familyName>Codegoni</familyName>
      <affiliation>University of Pavia</affiliation>
    </creator>
    <creator>
      <creatorName>Vercesi, Eleonora</creatorName>
      <givenName>Eleonora</givenName>
      <familyName>Vercesi</familyName>
      <affiliation>University of Pavia</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Single-Cell Gene Expression Profiles for Classification Problems</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>Gene-expression-profile, Leukemia, Brain, Pancreas, Gene Mover Distance</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-03-15</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4604569</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">http://arxiv.org/abs/2102.01218</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4604568</relatedIdentifier>
  </relatedIdentifiers>
  <version>v1.0.0</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;The three datasets are extracted from the Gene Expression Omnibus (GEO) database [2], where they appear, respectively,&amp;nbsp;with access number&amp;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.&lt;/p&gt;

&lt;p&gt;However, the proposed format should facilitate other researchers in using this data.&lt;/p&gt;

&lt;p&gt;The Gene Mover&amp;#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&amp;#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.&lt;/p&gt;

&lt;p&gt;The repository contains a python script to check the basic statistics of the data.&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;[1] Bellazzi, R., Codegoni, A., Gualandi, S., Nicora, G., Vercesi, E. &lt;em&gt;The Gene Mover&amp;#39;s Distance: Single-cell similarity via Optimal Transport&lt;/em&gt;. &lt;a href="https://arxiv.org/abs/2102.01218"&gt;https://arxiv.org/abs/2102.01218&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;[2] Gene Expression Omnibus (GEO) database, &lt;a href="http://www.ncbi.nlm.nih.gov/geo"&gt;http://www.ncbi.nlm.nih.gov/geo&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;[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. &lt;em&gt;Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity&lt;/em&gt;. Cell, 176(6), pp.1265-1281.&lt;/p&gt;

&lt;p&gt;[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.&lt;em&gt; A single-cell transcriptomic map of the human and mouse pancreas reveals inter-and intra-cell population structure&lt;/em&gt;. Cell systems, 3(4), pp.346-360.&lt;/p&gt;

&lt;p&gt;[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. &lt;em&gt;A survey of human brain transcriptome diversity at the single cell level&lt;/em&gt;. Proceedings of the National Academy of Sciences, 112(23), pp.7285-7290.&lt;/p&gt;</description>
  </descriptions>
</resource>
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