Integrated Center for Oncology

Breast Cancer Gene-Expression Miner v4.9
(bc-GenExMiner v4.9)

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Gene correlation targeted analysis Tutorial

Enter input genes and choose one of the following options:

  • GENES 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(s).
    For more than two genes, identifiers must be separated by ";" (e.g.: UBE2C;LMNB1).

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



  • DNA microarrays
    		• (n = 11 359)
    Clear allClear
  • RNA-seq
    		• (n = 4 421)

    		Open
    The uploaded file must comply with all following criteria:
    • file with tabulation, space, comma or newline separated values,
    • file type from among the following extensions: .csv, .tsv or .txt,
    • file containing only gene symbols (not full names or descriptions),
    • file with a maximum items of 20 gene symbols,
    • file with a maximum size of 10 Kbytes.

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

    This analysis is only available with DNA microarrays data (only Affymetrix™ data will be taken into account).
    This option allows you to split triple-negative breast cancer (TNBC) samples and explore their three subtypes: C1, C2 and C3:
    • C1: molecular apocrine tumours (or luminal androgen receptor);
    • C2: basal-like tumours infiltrated by immune suppressive cells and high neurogenesis activity;
    • C3: basal-like tumours triggering an ineffective immune response; which is associated with high tumour infiltrating lymphocytes and plasma cells, tertiary lymphoid structures and upregulation of immune checkpoints.
    More details about TNBC subtypes classification here.

  • 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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