preliminary results 2014-02-27. zoho page ki/465555000000561005/taz-yap-and- dpagt1-knockdown.html
TRANSCRIPT
Preliminary results
2014-02-27
Zoho page
• https://projects.zoho.com/portal/montilab#wiki/465555000000561005/TAZ-YAP-and-DPAGT1-knockdown.html
• (recommend: Firefox)
Microarray data analysis
• 1. QC• 2. clustering analysis• 3. identify differentially expressed genes in
each set• 4. simple enrichment analysis
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
Microarray data
• 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnsc
Microarray data
• 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnsc
– 1. Gsea enrichment with head-neck-cancer genesets
YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc
activated PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP
SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP
RICKMAN_HEAD_AND_NECK_CANCER_C
TAZ 0.915 0.586 /
YAP1 0.018 0.011 /
YAP1-TAZ 0 0.001 /
DPAGT1 0.031 / 0.089
YAP1 repressed genes overlap with up-regulated genes in hnsc
repressed RICKMAN_HEAD_AND_NECK_CANCER_A
RICKMAN_HEAD_AND_NECK_CANCER_C
RICKMAN_HEAD_AND_NECK_CANCER_E
TAZ 0.195 0.545 0.10
YAP1 0.188 0.196 0.003
YAP1-TAZ / 0.085 0.086
DPAGT1 / / 0.52
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
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)
YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc
activated PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP
SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP
RICKMAN_HEAD_AND_NECK_CANCER_C
TAZ 0.915 0.586 /
YAP1 0.018 0.011 /
YAP1-TAZ 0 0.001 /
DPAGT1 0.031 / 0.089
YAP1 activated genes showed higher level expression in tumors from TCGA
YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc
activated PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP
SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP
RICKMAN_HEAD_AND_NECK_CANCER_C
TAZ 0.915 0.586 /
YAP1 0.018 0.011 /
YAP1-TAZ 0 0.001 /
DPAGT1 0.031 / 0.089
YAP1-TAZ1 activated genes showed higher level expression in tumors from TCGA
YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc
activated PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP
SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP
RICKMAN_HEAD_AND_NECK_CANCER_C
TAZ 0.915 0.586 /
YAP1 0.018 0.011 /
YAP1-TAZ 0 0.001 /
DPAGT1 0.031 / 0.089
DPAGT1 activated genes showed higher level expression in tumors from TCGA (not very clear)
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)
YAP1 repressed genes overlap with up-regulated genes in hnsc
repressed RICKMAN_HEAD_AND_NECK_CANCER_A
RICKMAN_HEAD_AND_NECK_CANCER_C
RICKMAN_HEAD_AND_NECK_CANCER_E
TAZ 0.195 0.545 0.10
YAP1 0.188 0.196 0.003
YAP1-TAZ / 0.085 0.086
DPAGT1 / / 0.52
YAP1YAP1-TAZ
Microarray data
• 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnscConclusion: YAP1 and DPAGT1 activated genes seem to be differentially expressed in hnsc
Microarray data
• 1. whether we had evidence YAP1,TAZ,DPAGT1 may play a role in hnscConclusion: YAP1 and DPAGT1 regulated genes seem to be differentially expressed in hnsc
• 2. whether YAP1,TAZ, DPAGT1 are related with progression of the hnsc
Microarray signatures upon tumor progression in hnsc
• 1. heatmap of TCGA data using microarray signatures did not yield clear patterns
Microarray signatures upon tumor progression in hnsc
• 2. microarray signatures vs TCGA signatures
YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc
activated PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP
SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP
RICKMAN_HEAD_AND_NECK_CANCER_C
TAZ 0.915 0.586 /
YAP1 0.018 0.011 /
YAP1-TAZ 0 0.001 /
DPAGT1 0.031 / 0.089
YAP1 with TCGA signatures
G1+ vs normal
Up Down
YAP1- up Yes Yes
YAP1 - down Yes /
YAP1-TAZ -up Yes /
YAP1-TAZ -down Yes /
YAP activated genes does not seems to be correlated with tumor progression
G1+ vs normal G2+ vs G1 G3+ vs (G1&G2)
Up Down Up Down Up Down
YAP1- up Yes Yes / Yes / Yes
YAP1 - down Yes / Yes / Yes /
YAP1-TAZ -up Yes / / Yes / Yes
YAP1-TAZ -down Yes / Yes / Yes /
YAP1,DPAGT1 activated genes overlap with up-regulated genes in hnsc
activated PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP
SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP
RICKMAN_HEAD_AND_NECK_CANCER_C
TAZ 0.915 0.586 /
YAP1 0.018 0.011 /
YAP1-TAZ 0 0.001 /
DPAGT1 0.031 / 0.089
DPAGT1 with TCGA signatures
G1+ vs normal
Up Down
TAZ - up Yes /
TAZ - down Yes /
DPAGT1 -up / Yes
DPAGT1 -down Yes /
DPAGT1 activated genes does not seems to be correlated with tumor progression
G1+ vs normal G2+ vs G1 G3+ vs (G1&G2)
Up Down Up Down Up Down
TAZ - up Yes / / Yes / Yes
TAZ - down Yes / Yes / / /
DPAGT1 -up / Yes / Yes / Yes
DPAGT1 -down Yes / / Yes / Yes