Integrated Center for Oncology

Breast Cancer Gene-Expression Miner v4.7
(bc-GenExMiner v4.7)

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TNBC (IHC) subtypes prognostic analysis Tutorial

Enter input gene:

  • 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.

  • DNA microarrays
  • (n = 11 359)
  • (n = 693)
  • (n = 1 980)
  • RNA-seq
  • (n = 4 712)
  • (n = 1 034)
  • (n = 3 678)

  • Choose the characteristics (nodal, oestrogen and progesterone receptor status) of the cohorts to be explored.  "All" status includes patients with any status.

    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:
  • All time-to-event endpoints will be taken into account
    (DMFS, OS and DFS).
  • 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:

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