Applications of DrVAEN

1. TCGA

We predicted drug response for ~10,000 TCGA samples from 33 cancer types. The baseline transcriptome data were used as the input. All results, including response to 24 compounds from CCLE and 251 from GDSC, can be explored here.

2. GSE20194

Introduction: a dataset with 230 stage I-III breast cancers before any therapy.
Cancer type: breast cancer
Drug: paclitaxel
Data type: microarray
Analysis: predicted response in the pCR group and RD group

3. GSE25055

Introduction: a dataset with 310 HER2-negative breast cancer cases treated with taxane-anthracycline chemotherapy pre-operatively and endocrine therapy if ER-positive.
Cancer type: breast cancer
Drug: paclitaxel
Data type: microarray
Analysis: predicted response in the pCR group and RD group

4. GSE32646

Introduction: a dataset with primary breast cancer patients (n = 123, stage II-III) treated with neoadjuvant paclitaxel.
Cancer type: breast cancer
Drug: paclitaxel
Data type: microarray
Analysis: predicted response in the pCR group and RD group.

5. GSE32989

Introduction: non-small cell lung cancer (NSCLC) with 69 samples.
Cancer type: non-small cell lung cancer (NSCLC)
Drug: erlotinib
Data type: microarray
Analysis: predicted response in the Epithelial-like group and Mesenchymal-like group.

6. GSE33072

Introduction: 25 non-small cell lung cancer samples.
Cancer type: non-small cell lung cancer (NSCLC)
Drug: erlotinib
Data type: microarray
Analysis: survival analysis to compare the samples stratified by predicted response to erlotinib.

7. GSE65185

Introduction: transcriptomes from melanoma patient-matched tumor biopsies.
Cancer type: melanoma
Drug: PLX4720
Data type: RNA-seq
Analysis: survival analysis to compare the samples stratified by predicted response to PLX4720.