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miRNA gene regulatory networks for 38 human tissues

Kuijjer, Marieke Lydia; Quackenbush, John; Glass, Kimberly


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{
  "description": "<p>We reconstructed miRNA regulatory networks for 38 tissues from the Genotype-Tissue Expression project (GTEx) using two different prior networks, one obtained with target predictions from TargetScan and one with target predictions from miRanda.</p>\n\n<p>We used these networks to investigate gene expression and regulation by miRNAs across these tissues. In the RData file, we share the following objects:</p>\n\n<p>- <strong>exp</strong>: a 16,161 by 9,435 data frame including normalized expression data for each sample.</p>\n\n<p>- <strong>expTS</strong>: a 16,161 by 38 matrix including the tissue-specificity scores for each gene in each tissue.</p>\n\n<p>- <strong>netT</strong>: a 10,391,523 by 41 data frame that includes the miRNA regulatory networks. The column &quot;miRNA&quot; includes the name of the regulating miRNA, the column &quot;Gene&quot; includes the target gene (HGNC symbol), and the column &quot;Prior&quot; the prior regulatory network based on target predictions from TargetScan, with 1 for edges that are canonical and 0 for edges that are non-canonical. The remaining 38 columns contain the PUMA network edge weights for each of the 38 tissues.</p>\n\n<p>- <strong>netT_TS</strong>: a 10,391,523 by 38 matrix that includes the tissue-specificity scores of the miRNA regulatory networks that were modeled on the TargetScan prior. Edges are not labelled, but edge order corresponds to the edges in &quot;netT&quot;.</p>\n\n<p>- <strong>netM</strong>: a 10,391,523 by 41 data frame that includes the miRNA regulatory networks. The column &quot;miRNA&quot; includes the name of the regulating miRNA, the column &quot;Gene&quot; includes the target gene (HGNC symbol), and the column &quot;Prior&quot; the prior regulatory network based on target predictions from miRanda, with 1 for edges that are canonical and 0 for edges that are non-canonical. The remaining 38 columns contain the PUMA network edge weights for each of the 38 tissues.</p>\n\n<p>- <strong>netM_TS</strong>: a 10,391,523 by 38 matrix that includes the tissue-specificity scores of the miRNA regulatory networks that were modeled on the miRanda prior. Edges are not labelled, but edge order corresponds to the edges in &quot;netT&quot;.</p>\n\n<p>- <strong>samples</strong>: a 9,435 by 2 data frame that includes sample identifiers (matching the identifiers in &quot;exp&quot;) and the tissue to which these samples belong.</p>\n\n<p>- <strong>mirnames</strong>: a 694 by 3 data frame that contains miRNA names of regulators and their matching target miRNA names. The first column &quot;base_miRNA&quot; contains the &quot;base&quot; miRNA, the name of the miRNA without any extensions. The second column &quot;reg_miRNA&quot; contains the 643 regulator miRNA, which may have -3P/-5P extensions, and which matches the miRNAs that are present as regulators in the networks. The third columns &quot;tar_miRNA&quot; contains the 621 target miRNAs, which may have numbered suffix extensions, and for which we have expression data available.</p>", 
  "license": "https://creativecommons.org/licenses/by-nd/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Dana-Farber Cancer Institute, Harvard Chan School of Publich Health", 
      "@id": "https://orcid.org/0000-0001-6280-3130", 
      "@type": "Person", 
      "name": "Kuijjer, Marieke Lydia"
    }, 
    {
      "affiliation": "Dana-Farber Cancer Institute, Harvard Chan School of Publich Health", 
      "@id": "https://orcid.org/0000-0002-2702-5879", 
      "@type": "Person", 
      "name": "Quackenbush, John"
    }, 
    {
      "affiliation": "Channing Institute for Network Medicine, Brigham and Women's Hospital, Harvard Medical School", 
      "@type": "Person", 
      "name": "Glass, Kimberly"
    }
  ], 
  "url": "https://zenodo.org/record/1313768", 
  "datePublished": "2018-07-19", 
  "keywords": [
    "networks", 
    "gene regulatory networks", 
    "miRNA regulatory networks", 
    "gene regulation", 
    "miRNA", 
    "PUMA", 
    "PUMA networks"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/f9b1beef-0877-4f1a-99b2-c26395c010f6/GTEx_PUMA_tissues.RData", 
      "encodingFormat": "rdata", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.1313768", 
  "@id": "https://doi.org/10.5281/zenodo.1313768", 
  "@type": "Dataset", 
  "name": "miRNA gene regulatory networks for 38 human tissues"
}
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