Integrated Center for Oncology

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

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Gene correlation analysis by chromosomal location 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 or RNA-seq

    Then fill the textbox with actualised* gene symbol.

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

  • DNA microarrays
  • (n = 10 872)
  • RNA-seq
  • (n = 4 421)

  • POPULATION Open
  • Choose one of the radio button to select which population you want to explore.

    This analysis is only available with all DNA microarrays or all RNAseq data.
    This option allows to explore triple-negative breast cancer (TNBC) (IHC) subtypes (LAR, MLIA, BLIA and BLIS):
    • LAR: luminal androgen receptor,
    • MLIA: mesenchymal-like immune-activated,
    • BLIA: basal-like immune-activated,
    • BLIS: basal-like immune-suppressed.

  • OUTPUT CORRELATION 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:


  • Legend Open

     IHC:immunohistochemistry
     PAM50:Parker's instrinsic molecular subtypes
     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)
     TNBC:triple-negative breast cancer; tumours negative for oestrogen and progesterone receptors and epidermal growth factor receptor 2 (HER2), by means of IHC


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