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Tumor progression

Tumor progression. Early Adenoma. Hyperplastic Dysplastic. Polyp. Normal. Carcinoma. Metastasis (to Liver). COLON CANCER - TUMOR PROGRESSION:. Colon cancer - global view. First stage : Total of 144 micro-dissected samples Performed on Affymetrix GeneChip U133A (22,283 probe-sets).

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Tumor progression

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

  2. Colon cancer - global view First stage: Total of 144 micro-dissected samples Performed on Affymetrix GeneChip U133A (22,283 probe-sets) 22 Normal colon 24 polyp 47 primary cancer 19 lung metastasis 16 liver metastasis 5 normal lung 11 normal liver

  3. Colon cancer – PCA First stage: Total of 144 micro-dissected samples Performed on Affymetrix GeneChip U133A (22,283 probe-sets) 22 Normal colon 24 polyp 47 primary cancer 19 lung metastasis 16 liver metastasis 5 normal lung 11 normal liver 1st PCA: tissue 2nd PCA: transformation 3rd PCA: muscle/connective contamination 2 of the dominant signals are not relevant

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

  5. expression levels of 2 genes for 4 patients: • (19) (27) (37) • 9 11 3 • 8 2 4 6 Gene 1 Gene 2 (27) 4 POINTS IN 2-DIMENSIONS: (19) 4 points Gene 2 Gene 1

  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. Colon cancer – PCA First stage: Total of 144 micro-dissected samples Performed on Affymetrix GeneChip U133A (22,283 probe-sets) 22 Normal colon 24 polyp 47 primary cancer 19 lung metastasis 16 liver metastasis 5 normal lung 11 normal liver 1st PCA: tissue 2nd PCA: transformation 3rd PCA: muscle/connective contamination 2 of the dominant signals are not relevant

  13. Colon - 1,000 highest variance genes

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

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

  16. (27) (19) 4 points

  17. 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 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

  18. (5) (19) (27) (37) (5) (37) (19) (27) 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

  19. Aug 2000 Bittner Yakhini MDS

  20. glioblastoma 174 genes separate (at FDR of 5%) PrGBM from LGA + ScGBM 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 GLIOBLASTOMA: CLONTECH ARRAYS 1185 Genes, 36 Samples 12 Astrocytoma(II) 4 secondary GBM 17 Primary GlioBlastoMa 3 Cell Lines

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