1. Early Adenoma Normal Hyperplasti c Dysplastic Carcinoma Polyp Metastasis (to Liver) COLON CANCER - TUMOR PROGRESSION: Tumor progression

2. 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

3. 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) 1 st PCA: tissue 2 nd PCA: transformation 3 rd PCA: muscle/connective contamination 2 of the dominant signals are not relevant Colon cancer – PCA

4. SPIN: MOTIVATION GLOBAL LAYOUT OF DATA IDENTIFY RELEVANT SUBSETS OF GENES SHAPES OF DATA “CLOUDS” DEMONSTRATE ON COLON CANCER DATA SORTING liver met lung met colon polyp carc.

5. 4 points Gene 1 Gene 2 expression 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)

6. project on y

7. project on x

8. PCA Projection with Maximal Variance:

9. Pitas.fig

10. PCA leukemia 1 Korsmeyer ALL,AML,MLL 8700 genes Nature 2001

11. PCA Leukemia 2 Korsmeyer ALL,AML,MLL (In space of 500 most separating genes)

12. 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) 1 st PCA: tissue 2 nd PCA: transformation 3 rd PCA: muscle/connective contamination 2 of the dominant signals are not relevant Colon cancer – PCA

13. Colon - 1,000 highest variance genes

14. 45 samples 17,300 probes PCA 1 PCA 2 PCA 3 Cervical Cancer - Gene Expression Matrix 5 Normal cervical tissues 35 Tumors (5 repeats) 5 Cancer cell lines

15. Focus on relevant samples PCA 2 PCA 1 PCA 3 Removed the cell lines, the normals, the a6g (29-3) that clustered with the normals; kept 1 of each repeat 29 samples 17,300 probes

16. 4 points (27) (19)

17. toy distmat 0.0 10.0 10.77 2.82 10.0 0.0 2.82 7.21 10.77 2.82 0.0 8.24 2.82 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)

18. toy distmat ordered 0.0 10.0 10.77 2.82 10.0 0.0 2.82 7.21 10.77 2.82 0.0 8.24 2.82 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)

19. Bittner Yakhini MDS Aug 2000

20. 17 Primary GlioBlastoMa 3 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