Integrated Center for Oncology

Breast Cancer Gene-Expression Miner v5.1
(bc-GenExMiner v5.1)

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Intrinsic molecular subtypes prognostic analysis Tutorial

Enter input gene and 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)

    Then fill the textbox with actualised* gene symbol or Affymetrix® probeset ID.

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

    @: the probesets followed by "@" are described as references for subtyping ER, PR and HER2 status by means of transcriptomics data. See Kenn et al..

  • DNA microarrays
    		• (n = 10 872)
  		• (n = 5 183)
  		• (n = 1 980)
  • RNA-seq
    		• (n = 4 421)
  		• (n = 743)
  		• (n = 3 678)

  • INTRINSIC MOLECULAR SUBTYPING METHOD Open
    • Choose one of the radio button to select which intrinsic molecular subtyping method you want to explore: "All" (all intrinsic molecular subtypes), "SSPs and RSSPC" or "SCMs and RSCMC". More details.

  • Subtyping gene signatures:
  • POPULATION Open
    • Choose the kind of event used for survival analyses:
    • "distant metastasis-free survival" (DMFS): first pejorative event represented by distant relapse.
    • "overall survival" (OS): first pejorative event represented by death.
    • "disease-free survival" (DFS): first pejorative event represented by any relapse or death.
    These datasets are retrieved from published annotated transcriptomic data.

  • Event status:
  • DISCRETISATION Open
    • Choose one of the radio button to select which splitting method you want to explore for prognostic 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:


    • Legend Open
     All:all methods below-listed
     DFS:disease-free survival
     DMFS:distant metastasis-free survival
     OS:overall survival (any relapse or death)
     RIMSPC:robust intrinsic molecular subtype predictors classification based on patients classified in the same subtype with the six molecular subtype predictors (3 SSPs + 3 SCMs)
     RSCMC:robust SCM classification based on patients classified in the same subtype with the three SCMs
     RSSPC:robust SSP classification based on patients classified in the same subtype with the three SSPs
     SCM:Subtype clustering model (SCMOD1, SCMOD2 or SCMGENE)
     SSP:single sample predictor (Sorlie's, Hu's or PAM50)


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