Integrated Center for Oncology

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

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Targeted expression 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.

    *: 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)

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

    This analysis is only available with TCGA data.
    This option allows you to split samples by the nature of the tissue.
    There are nine distinct analysis possibilities, each time comparing healthy (or normal) versus tumour-adjacent versus:
    • tumour tissue;
    • oestrogen receptor status;
    • progesterone receptor status;
    • oestrogen/progesterone receptor status combinations;
    • HER2 receptor status;
    • P53 status (sequence-based);
    • PAM50 breast cancer subtypes;
    • TNBC/non-TNBC;
    • triple-negative breast cancer (IHC) & basal-like (PAM50).

    This analysis is only available with All microarray, Affymetrix™, METABRIC and TCGA data.

    This analysis is only available with TCGA data.
    Pathological tumor stage according to American Joint Committee on Cancer (AJCC).

    This analysis is only available with All microarray, Affymetrix™, METABRIC and SCAN-B data
    Scarff, Bloom & Richardson grade.

    This analysis is only available with All microarray, Affymetrix™, METABRIC and SCAN-B data
    Nottingham prognostic index.

    51 years old has been chosen as it is median age at menopause in western industrialised countries.

    This analysis is only available with Affymetrix™ and SCAN-B data.
    A threshold of ≥ 20% is indicative of high Ki67 status (Goldhirsch et al., 2013).

    This analysis is only available with All microarray, Affymetrix™, METABRIC and TCGA data.

    This analysis is only available with All microarray, METABRIC and TCGA data.

    This analysis split patients into groups bounded by multiple intrinsic molecular subtyping methods : "SSPs and RSSPC", "SCMs and RSCMC" and "RIMSPC". More details.

    This analysis is only available with all type of 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-altered,
    • BLIA: basal-like immune-activated,
    • BLIS: basal-like immune-suppressed.

    This analysis is only available with METABRIC data.
    It permits to compare gene expression in the 10 or 11 integrative clusters (IntClust = iC) Curtis et al., 2012 and Dawson et al., 2013.

  • 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:


    • Legend Open
     ER:oestrogen receptor
     GES:gene expression signature
     HER2:HER2 receptor
     IHC:immunohistochemistry
     NPI:Nottingham prognostic index
     PAM50:Parker's instrinsic molecular subtypes
     PR:progesterone receptor
     SBR:Scarff, Bloom & Richardson grade
     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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