Integrated Center for Oncology

Breast Cancer Gene-Expression Miner v5.0
(bc-GenExMiner v5.0)

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Customised expression analysis Tutorial

Enter input genes to analyse (reference in second textbox), then choose one of the following options:

  • GENE EXPRESSION DATA Open
    • First, choose your gene expression data. Information about cohorts : microarrays, Affymetrix®, METABRIC, TCGA or SCAN-B (aka GSE81540 = GSE81538 + GSE96058)
    This is your target gene. Its expression values will be split by another gene (see below).
    Nota bene: only Affymetrix® U133 Plus 2.0 have been retained for this analysis module (if Affymetrix data are chosen).

    *: see actualised web databases (e.g.: Ensembl, GeneCards, HGNC, NCBI Gene...)

  • DNA microarrays
    		• (n = 10 872)
  		• (n = 2 151)
  		• (n = 1 980)
  • RNA-seq
    		• (n = 4 421)
  		• (n = 743)
  		• (n = 3 678)

  • SPLITTING GENE Open
    • This gene will be dichotomised according to chosen splitting criterion expression value (option below), and will be the splitting criteria of the tested gene (first textbox).
    Fill the textbox with actualised* gene symbol that will be your splitting criteria.

    *: see actualised web databases (e.g.: Ensembl, GeneCards, HGNC, NCBI Gene...)


  • DISCRETISATION Open
    • Choose one of the radio button to select which splitting method you want to explore for expression study:
    • "mediane": 2 groups split at 50%,
    • "tertile": 3 groups split at 33%,
    • "quartile": 4 groups split at 25%,
    • "optimal": 2 groups split at the best cut-off (more details)
    • "custom percentile": 2 groups split at the user cut-off.

  • Splitting criterion:
  • OUTPUT EXPRESSION FIGURE Open
    • Choose one of the radio button to select which output figure you want to get as a result plot.
    Have a sneak peak of each figure by clicking on following options available:

  • Type of plot:


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