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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

 
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BMC Bioinformatics

ISSN: 1471-2105

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