PDXGEM:
Select Biomarker Discovery Set
Novartis
else
Select Human Cancer Type for drug response prediction
Breast
Pancreatic
Colorectal
NSCLC
Step 1: In vivo PDX Drug Sensitivity Biomarkers
Step 1: Select a method for initial drug sensitivity biomarkers
correlation
correlation-rank
t-test
t-test_binary_at_zero
else
Download
Step 2: CCEA analysis of drug sensitivity biomarkers
Adjust a threhold of CCEC
Download
Do you want to filter initial drug sensitivity biomarkers by Concordant Co-Expression Analysis?
Yes
No
Step 3: Builing a multi-gene expression model for predictin a clinical response to the drug of interest
Select response transformation
None
rank-transform
Step 3-1: Training Random Forest-based model (PDXGEM) training
Download RF importance
Download RF predictor
Step 3-2: Validation of PDXGEM on an indepenent patient cohort
Choose CSV or Tab delimited File
Browse...
Select a Model Test set
BR:GSE20194(MAQCII)
BR:GSE41998:Horak(paclitaxel)
BR:GSE20271:Tabchy(TFAC)
BR:GSE20271:Tabchy(FAC)
BR:GSE25065:Hatzis
BR:GSE32646:Miyake
BR:GSE42822:USO(FAC+TX)
BR:GSE42822:USO(FAC+TX+Trastuzumab)
BR:GSE22226:I-SPY(ACT+Trastuzumab)
BR:GSE22358:Agilent:Trastuzumab
CRC:Khambata(Cetuximab)
CRC:Khambata:KRASwild(Cetuximab)
CRC:Khambata:KRASmutation(Cetuximab)
CRC_GSE62322_FOLFIRI_Metastasis
CRC_GSE39582_5FU+FOLFIRI
CRC_GSE39582_5FU+FOLFIRI_Metastasis
CRC_GSE39582_5FU+FOLFIRI_NoMetastasis
CRC_GSE39582_5FU_NoMetastasis
CRC_GSE39582_FOLFIRI_Metastasis
CRC_GSE39582_FOLFIRI_NoMetastasis
CRC_GSE52735_Fluoropyrimidine
CRC_GSE14095_LiverMetastasis
CRC_GSE19860_Metastasis_FOLFOX+Bevacizumab
NSCLC:GSE31625CellLines:Erlotinib
NSCLC:GSE37138:Bevacizumab+Erlotinib
NSCLC:GSE33072:BATTLE(Sorafenib|Erlotinib)
NSCLC:GSE33072:BATTLE(All)
NSCLC:GSE68793:TCGA:NoErlotinib
HNSCC_GSE65021(Illumina)_Cetuximab
Pancreatic:GSE57495:Moffitt
Pancreatic:EMEXP2780
Pancreatic:GSE17891:Patient
Pancreatic_GSE28735_HuEXst1
Pancreatic:ICGC_RNAseq
Download a validation results (GEM score and clinical outcomes)
Step 3: Model validation