Early Adenoma Normal 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

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

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.

4 points Gene 1 Gene 2 expression levels of 2 genes for 4 patients: (5)(19) (27) (37) Gene 1 Gene 2 4 POINTS IN 2-DIMENSIONS: (27) (19)

project on y

project on x

PCA Projection with Maximal Variance:

Pitas.fig

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

PCA Leukemia 2 Korsmeyer ALL,AML,MLL (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) 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

Colon - 1,000 highest variance genes

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

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

4 points (27) (19)

toy distmat (5) (19) (27) (37)

toy distmat ordered (5) (19) (27) (37) (5) (37) (19) (27)

Bittner Yakhini MDS Aug 2000

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