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Table 1 Clinical characteristics of k = 2,3,7 clusters: The ER, PR, Her2, Node, stage and grade status of the samples in each cluster are shown for k = 2,3 and 7. ND stands for "Not Determined". At k = 2, the clustering splits the data into normal samples and disease samples (BCA), except for one ADH which is classified with the normals. At k = 3, the BCA samples split into high grade (grade 2 or 3) and low grade (grade 1 or 2) categories. At k = 7, the low grade samples split into two clusters LG1, LG2 and the high grade into four: HG1 – HG4. The HG1 samples are all ER-, PR- and mostly Her2-. The HG3 and HG4 clusters are mostly ER+, PR+, Her2-. The HG2 cluster has mixed ER, PR and Her2 signatures. Using the Sorlie et al classification, we identify HG1 as the Basal-like subtype; LG1 as Luminal A; LG2, HG3 and HG4 as Luminal B and HG2 as the Her2+ subtype. When the sum of the entries for ER/PR/Her2/Node/Grade do not add up to the size of the cluster, it is because the corresponding information was missing in the dataset [10].

From: Portraits of breast cancer progression

Cluster level k Group Size Stage ER PR Her2 Node Grade
    ADH DCIS IDC N Pos Neg ND Pos Neg ND Pos Neg ND Pos Neg 1 2 3
2 N 33 1    32               
  BCA 60 7 30 23   47 10 3 42 15 3 10 37 9 44 14 18 22 19
3 LG 28 7 13 8   26   2 21 5 2 4 18 6 20 8 18 9  
  HG 32   17 15   21 10 1 21 10 1 6 19 3 24 6   13 19
7 LG1 11 4 5 2   11    8 3   1 10   7 4 9 2  
  LG2 17 3 8 6   15   2 13 2 2 3 8 6 13 4 9 7  
  HG1 5   2 3    5    5   1 4   3     5
  HG2 10   7 3   7 3   5 5   3 4 1 9 1   2 8
  HG3 13   6 7   10 2 1 12   1 2 7 2 10 3   7 6
  HG4 4   2 2   4    4     4   2 2   4