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].
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

Dalgin et al. BMC Bioinformatics 2007 8:291   doi:10.1186/1471-2105-8-291