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Table 2 Chromowave and FISH results for the glioma data-set.

From: Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas

Case

Diagnosis

FISH Load Chr1p36

Chromowave Load Chr1 (+ = loss)

FISH Load Chr4c

Chromowave Load Chr4 (+ = loss)

FISH Load Chr9q34

Chromowave Load Chr9 (+ = loss)

FISH Load Chr13q14

Chromowave Load Chr13 (+ = loss)

FISH Load Chr15c

Chromowave Load Chr15 (+ = loss)

FISH Load Chr18c

Chromowave Load Chr18 (+ = loss)

FISH Load Chr19q13

Chromowave Load Chr19 (+ = loss)

Gender

Chromowave Load ChrY (+ = loss)

1

OII (O1)

Mono

0.21

 

0.03

 

0.06

 

0.08

 

0.06

 

0.02

Mono

0.37

M

-0.20

2

OII (O20)

Mono

0.17

 

-0.15

 

0.25

 

-0.22

 

-0.18

 

0.40

Mono

0.20

F

0.22

3

OII (O4)

Mono

0.09

 

0.00

 

-0.01

 

-0.01

 

-0.16

 

0.03

 

0.03

F

0.14

4

OII (O23)

 

0.04

Mono

0.00

 

-0.19

 

-0.18

 

-0.22

 

-0.17

Mono

0.02

F

0.17

5

OAII (O19)

 

0.09

 

-0.22

 

-0.18

 

-0.32

 

-0.14

 

-0.19

Mono

0.16

M

-0.28

6

OAII (O15)

 

-0.17

 

-0.15

 

0.42

 

-0.19

 

-0.12

 

-0.08

 

-0.51

M

-0.22

7

OII (O10)

 

0.25

 

0.15

 

0.14

Mono

0.26

 

0.03

 

0.14

 

0.2

F

0.18

8

OAII (O7)

 

-0.04

 

0.06

 

0.07

Mono

0.30

Mono

0.11

 

-0.02

 

0.01

M

-0.24

9

OAII (O8)

 

-0.19

 

-0.12

Mono

0.08

Mono

0.03

 

-0.24

 

-0.19

 

-0.22

M

-0.16

10

OAII (O6)

 

-0.06

NA

0.20

 

-0.01

 

0.04

 

0.1

 

0.05

 

0.1

F

0.16

11

OII (O16)

 

-0.08

 

-0.12

 

0.12

 

-0.08

 

-0.01

 

0.06

 

0.05

F

0.23

13

AII (AD6)

 

-0.08

 

-0.01

 

-0.12

 

-0.12

 

0.03

 

-0.02

 

-0.12

M

-0.20

14

AII (AD9)

 

-0.12

 

-0.04

 

-0.07

 

-0.04

 

0.01

 

-0.07

 

0.07

M

-0.22

15

AII (AD10)

 

-0.15

 

-0.12

 

-0.23

 

-0.22

 

-0.1

 

-0.17

 

-0.13

M

-0.20

16

AII (AD11)

Mono

0. 1

 

0.12

 

0.12

 

0.12

Mono

0.27

 

0.09

 

0.01

M

-0.19

17

AII (AD12)

 

-0.11

 

-0.09

 

-0.01

 

-0.14

 

-0.01

 

-0.13

 

-0.12

M

-0.21

18

OIII (O2)

Mono

0.09

 

0.28

Mono

-0.23

Mono

0.27

 

-0.22

 

0.00

Mono

0.03

F

0.20

19

OIII (O3)

Mono

0.33

Mono

0.64

 

0.14

Mono

0.48

Mono

0.05

Mono

0.68

Mono

0.06

M

0.01

20

OIII (O17)

Mono

0.27

 

-0.05

 

0.17

Mono

-0.10

Mono

-0.08

 

-0.07

Mono

0.4

F

0.18

21

OIII (O18)

Mono

-0.16

 

-0.15

 

-0.13

 

-0.17

Mono

0.22

 

-0.16

 

-0.36

F

0.13

22

OIII (O9)

Mono

0.31

 

0.19

 

0.23

 

0.11

Mono

0.7

 

0.09

Mono

0.02

F

0.19

23

OAIII (O24)

 

-0.15

 

-0.14

 

-0.17

 

-0.14

Mono

0.03

 

-0.17

 

-0.19

M

-0.22

24

OIII (O12)

 

-0.17

 

0.29

 

-0.04

 

0.30

 

0.25

 

0.19

 

0.03

F

0.13

25

AIII (AA3)

 

-0.15

 

-0.10

 

-0.48

 

0.02

 

-0.11

 

-0.26

 

-0.1

F

0.25

26

AIII (AA6)

 

-0.07

 

-0.04

 

0.32

 

0.15

 

-0.11

 

0.09

 

-0.03

F

0.15

27

AIII (AA5)

 

-0.05

 

-0.30

 

-0.10

 

-0.10

 

-0.08

 

-0.04

 

0.09

M

-0.18

  1. This table illustrates the combined variation of gene expression of chromosomes 1p, 4, 9p, 13, 15, 18, 19q detected by CHROMOWAVE and the variations detected by FISH analysis. Note that the case-loadings reflect the normalization to the average that is performed by the SVD. Therefore, the more positive the case loading is the greater is the loss. As a rule of thumb loadings close to or grater than zero indicate monosomy. Positive cases are highlighted in bold. Cases underlined are hyperploid and cases highlighted in italics showed a discrepancy between FISH and CHROMOWAVE (loss detected in FISH not detected by CHROMOWAVE) – O: Oligodendroglioma – OA: Oligoastrocytoma – A: Astrocytoma – AA: Anaplastic astrocytoma; II grade II, III grade III – NA: not available.
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