Early

AdenomaNormal Hyperplasti

c

Dysplastic

Carcinoma Polyp Metastasis

(to Liver)

COLON CANCER - TUMOR PROGRESSION:

Tumor progression

22 Normal colon

24 polyp

47 primary cancer

19 lung metastasis

16 liver metastasis

5 normal lung

11 normal liver

First stage: Total of 144 micro-dissected samples Performed on Affymetrix GeneChip U133A (22,283 probe-sets)

Colon cancer - global view

Expression 1-99%

20 40 60 80 100 120 140

100

200

300

400

500

600

700

800

900

1000

22 Normal colon

24 polyp

47 primary cancer

19 lung metastasis

16 liver metastasis

5 normal lung

11 normal liver

First stage: Total of 144 micro-dissected samples Performed on Affymetrix GeneChip U133A (22,283 probe-sets)

1st PCA: tissue2nd PCA: transformation3rd PCA: muscle/connective contamination2 of the dominant signals are not relevant

Colon cancer – PCA

SPIN: MOTIVATION

GLOBAL LAYOUT OF DATA

IDENTIFY RELEVANT SUBSETS OF GENES

SHAPES OF DATA “CLOUDS”

DEMONSTRATE ON COLONCANCER DATA

Expression 1-99%

20 40 60 80 100 120 140

100

200

300

400

500

600

700

800

900

1000

SORTINGExpression 1-99%

A

B

H

K

M

U

V

100

200

300

400

500

600

700

800

900

1000

livermetlungmetcolonpolypcarc.

4 points

Gene 1

Gen

e 2expression levels of 2 genes

for 4 patients:

(5) (19) (27) (37)

1 9 11 3 8 2 4 6

Gene 1

Gene 2

4 POINTS IN 2-DIMENSIONS:

(27)

(19)

project on y

project on x

PCA

Projection withMaximal Variance:

-2 0 2 4 6 8 10 12

-8

-6

-4

-2

0

2

4

6

Pitas.fig

PCA leukemia 1

KorsmeyerALL,ALL,AML,AML,MLLMLL8700 genes

Nature 2001

PCA Leukemia 2

Korsmeyer

ALL,ALL,AML,AML,MLLMLL

(In space of 500 most separating genes)

22 Normal colon

24 polyp

47 primary cancer

19 lung metastasis

16 liver metastasis

5 normal lung

11 normal liver

First stage: Total of 144 micro-dissected samples Performed on Affymetrix GeneChip U133A (22,283 probe-sets)

1st PCA: tissue2nd PCA: transformation3rd PCA: muscle/connective contamination2 of the dominant signals are not relevant

Colon cancer – PCA

Colon - 1,000 highest variance genes

-10 -5 0 5 10

-10

-5

0

5

10

PCA 1

PC

A 2

45 samples

17,3

00 p

robe

s

-30

-20

-10

0

10

-10

0

10

20

-15

-10

-5

0

5

10

15

20

25

a8b a8o

PCA 2 PCA 1

e8b a8b

a8g a8+

a8g

a6o e6b a6g a8b

a6g

e6b e6b

e8g

e6g

e6b

e8b e6b

e6b

e8g

e8b e8b

e6g

e6g

e6g e6g

e6b e6b

c8o

e8g

e3b c8o

e6g

a6g

e6+

e9o c6o

c8o

c6o

noo

PC

A 3

noo

noo noo

noo

PCA 1PCA 2

PC

A 3

Cervical Cancer - Gene Expression Matrix

5 Normal cervical tissues35 Tumors (5 repeats) 5 Cancer cell lines

Focus on relevant samples

-15-10

-50

510

15-10

-5

0

5

10

15-10

-5

0

5

10

e6g a8b

e8b

a8b

PCA 1

PCA 2

e6b

a8o

e6+

a8g

a6g

e6b

e6g

e8b

e6b

e8g e6b

e8g

e6g

a8b e8g

e6g

e6b

e3b

e9o

a6g

a6o

a8+

e8b

e6b e6g

PC

A 3

PCA 2PCA 1

PC

A 3

Removed the cell lines, the normals, the a6g (29-3) that clustered with the normals; kept 1 of each repeat29 samples

17,3

00 p

robe

s

4 points

(27)

(19)

toy distmat

0.0 10.0 10.77 2.8210.0 0.0 2.82 7.2110.77 2.82 0.0 8.242.82 7.21 8.24 0.0

0.0 2.82 10.0 10.77 10.0 7.21 0.0 2.82

10.77 8.24 2.82 0.0 2.82 0.0 7.21

8.24 0.0 2.82 10.0 10.77

2.82 0.0 7.21 8.24 10.0 7.21 0.0 2.82

10.77 8.24 2.82 0.0

(5) (19) (27) (37)

toy distmat ordered

0.0 10.0 10.77 2.8210.0 0.0 2.82 7.2110.77 2.82 0.0 8.242.82 7.21 8.24 0.0

0.0 2.82 10.0 10.77 2.82 0.0 7.21 8.24

10.0 7.21 0.0 2.82 10.77 8.24 2.82 0.0

(5) (19) (27) (37) (5) (37) (19) (27)

Bittner Yakhini MDS

Aug 2000

17 Primary GlioBlastoMa3 Cell Lines

1185 Genes, 36 Samples

GLIOBLASTOMA:

glioblastoma

CLONTECH ARRAYS

S Godard, G Getz, H Kobayashi, P Farmer, M Delorenzi, M Nozaki, A-C Diserens, M-F Hamou, P-Y Dietrich, J-G Villemure, R C. Janzer,

P Bucher, R Stupp, N de Tribolet, E Domany, M E. Hegi

12 Astrocytoma(II) 4 secondary GBM

174 genes separate (at FDR of 5%) PrGBM from LGA + ScGBM

-3

-2

-1

0

1

2

3

4

5 10 15 20 25 30

100

200

300

400

500

600

700

800

900

1000

1100