Integrated Center for Oncology

Breast Cancer Gene-Expression Miner v4.2
(bc-GenExMiner v4.2)

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Molecular subtype prognostic analysis Tutorial

Enter input gene and choose the following option:

  • GENE Open
  • Fill the textbox with actualised* gene symbol or Affymetrix probeset ID.

    *: see actualised web databases (e.g.: GeneCards, Source, Unigene...)

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

  • Choose one of the radio button to select which molecular subtyping method you want to explore: "SSP", "SCM" or "All".
    More information about molecular subtyping here.

  • 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 info)
    • "custom percentile": 2 groups split at the user cut-off.

  • Splitting criterion:

  • Legend  Open

     All: all methods below-listed
     SCM: Subtype Clustering Model (SCMOD1, SCMOD2 and SCMGENE)
     SSP: Single Sample Predictor (Sorlie's, Hu's and PAM50)

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