Integrated Center for Oncology

Breast Cancer Gene-Expression Miner v4.5
(bc-GenExMiner v4.5)

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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.: GeneCards, Ensembl, HGNC, NCBI Gene...)

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

  • DNA microarrays
    		• (n = 10 001)
  		• (n = 4 904)
  		• (n = 1 980)
  • RNA-seq
    		• (n = 4 712)
  		• (n = 1 034)
  		• (n = 3 678)

  • POPULATION Open
    • Choose one of the radio button to select which splitting method you want to explore for all patients.
    Note: 51 years old is median age at menopause in western industrialised countries.
    More details about molecular subtypes here.

    This analysis is only available with TCGA data.
    This option allows you to split samples by the nature of the tissue.
    There are 9 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;
    • basal-like (PAM50) & triple-negative breast cancer (IHC).

    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 Affymetrix™ data.
    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.

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



    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 growth factor receptor 2 (HER2), by means of IHC.


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