1. Preliminary results 2014-02-27

2. Zoho page https://projects.zoho.com/portal/montilab#wi ki/465555000000561005/TAZ-YAP-and- DPAGT1-knockdown.html https://projects.zoho.com/portal/montilab#wi ki/465555000000561005/TAZ-YAP-and- DPAGT1-knockdown.html (recommend: Firefox)

3. Microarray data analysis 1. QC 2. clustering analysis 3. identify differentially expressed genes in each set 4. simple enrichment analysis

4. Microarray data analysis(cont.) 5. enrichment analysis (gsea approach) 6. evaluate the connection between microarray-derived signatures vs TCGA derived signatures 7. apply microarray-derived signatures to TCGA raw data

5. Microarray data 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnsc

6. Microarray data 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnsc – 1. Gsea enrichment with head-neck-cancer genesets

7. YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc activatedPYEON_CANCER_ HEAD_AND_NECK _VS_CERVICAL_U P SLEBOS_HEAD_A ND_NECK_CANCE R_WITH_HPV_UP RICKMAN_HEAD_ AND_NECK_CANC ER_C TAZ0.9150.586/ YAP10.0180.011/ YAP1-TAZ00.001/ DPAGT10.031/0.089

8. YAP1 repressed genes overlap with up- regulated genes in hnsc repressedRICKMAN_HEAD _AND_NECK_CA NCER_A RICKMAN_HEAD _AND_NECK_CA NCER_C RICKMAN_HEAD _AND_NECK_CA NCER_E TAZ0.1950.5450.10 YAP10.1880.1960.003 YAP1-TAZ/0.0850.086 DPAGT1//0.52

9. Microarray data 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnsc – 1. Gsea enrichment with head-neck-cancer genesets – 2. examine the differentially expressed genes in TCGA dataset

10. Microarray data 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnsc – 1. Gsea enrichment with head-neck-cancer genesets – 2. examine the differentially expressed genes in TCGA dataset (activated/repressed genes)

11. YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc activatedPYEON_CANCER_ HEAD_AND_NECK _VS_CERVICAL_U P SLEBOS_HEAD_A ND_NECK_CANCE R_WITH_HPV_UP RICKMAN_HEAD_ AND_NECK_CANC ER_C TAZ0.9150.586/ YAP10.0180.011/ YAP1-TAZ00.001/ DPAGT10.031/0.089

12. YAP1 activated genes showed higher level expression in tumors from TCGA

13. YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc activatedPYEON_CANCER_ HEAD_AND_NECK _VS_CERVICAL_U P SLEBOS_HEAD_A ND_NECK_CANCE R_WITH_HPV_UP RICKMAN_HEAD_ AND_NECK_CANC ER_C TAZ0.9150.586/ YAP10.0180.011/ YAP1-TAZ00.001/ DPAGT10.031/0.089

14. YAP1-TAZ1 activated genes showed higher level expression in tumors from TCGA

15. YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc activatedPYEON_CANCER_ HEAD_AND_NECK _VS_CERVICAL_U P SLEBOS_HEAD_A ND_NECK_CANCE R_WITH_HPV_UP RICKMAN_HEAD_ AND_NECK_CANC ER_C TAZ0.9150.586/ YAP10.0180.011/ YAP1-TAZ00.001/ DPAGT10.031/0.089

16. DPAGT1 activated genes showed higher level expression in tumors from TCGA (not very clear)

17. Microarray data 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnsc – 1. Gsea enrichment with head-neck-cancer genesets – 2. examine the differentially expressed genes in TCGA dataset (activated/repressed genes)

18. YAP1 repressed genes overlap with up- regulated genes in hnsc repressedRICKMAN_HEAD _AND_NECK_CA NCER_A RICKMAN_HEAD _AND_NECK_CA NCER_C RICKMAN_HEAD _AND_NECK_CA NCER_E TAZ0.1950.5450.10 YAP10.1880.1960.003 YAP1-TAZ/0.0850.086 DPAGT1//0.52

19. YAP1 YAP1-TAZ

20. Microarray data 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnsc Conclusion: YAP1 and DPAGT1 activated genes seem to be differentially expressed in hnsc

21. Microarray data 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnsc Conclusion: YAP1 and DPAGT1 regulated genes seem to be differentially expressed in hnsc 2. whether YAP1,TAZ, DPAGT1 are related with progression of the hnsc

22. Microarray signatures upon tumor progression in hnsc 1. heatmap of TCGA data using microarray signatures did not yield clear patterns

23. Microarray signatures upon tumor progression in hnsc 2. microarray signatures vs TCGA signatures

24. YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc activatedPYEON_CANCER_ HEAD_AND_NECK _VS_CERVICAL_U P SLEBOS_HEAD_A ND_NECK_CANCE R_WITH_HPV_UP RICKMAN_HEAD_ AND_NECK_CANC ER_C TAZ0.9150.586/ YAP10.0180.011/ YAP1-TAZ00.001/ DPAGT10.031/0.089

25. YAP1 with TCGA signatures G1+ vs normal UpDown YAP1- upYes YAP1 - downYes/ YAP1-TAZ -upYes/ YAP1-TAZ -downYes/

26. YAP activated genes does not seems to be correlated with tumor progression G1+ vs normalG2+ vs G1G3+ vs (G1&G2) UpDown UpDownUpDown YAP1- upYes / / YAP1 - downYes/ / / YAP1-TAZ -upYes// / YAP1-TAZ -downYes/ / /

27. YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc activatedPYEON_CANCER_ HEAD_AND_NECK _VS_CERVICAL_U P SLEBOS_HEAD_A ND_NECK_CANCE R_WITH_HPV_UP RICKMAN_HEAD_ AND_NECK_CANC ER_C TAZ0.9150.586/ YAP10.0180.011/ YAP1-TAZ00.001/ DPAGT10.031/0.089

28. DPAGT1 with TCGA signatures G1+ vs normal UpDown TAZ - upYes/ TAZ - downYes/ DPAGT1 -up/Yes DPAGT1 -downYes/

29. DPAGT1 activated genes does not seems to be correlated with tumor progression G1+ vs normalG2+ vs G1G3+ vs (G1&G2) UpDown UpDownUpDown TAZ - upYes// / TAZ - downYes/ /// DPAGT1 -up/Yes/ / DPAGT1 -downYes// /