Example Queries
Browse example queries by analysis type to learn how to get the most out of BioQuery.
Quick Reference
| Analysis Type | Example Query |
|---|---|
| Differential Expression | ”Is EGFR higher in LUAD vs LUSC?” |
| Tumor vs Normal | ”Is MYC upregulated in breast cancer?” |
| Mutation Frequency | ”What’s the TP53 mutation rate in GBM?” |
| Survival Analysis | ”Does high DDR1 predict worse survival?” |
| Cell Line Expression | ”DDR1 expression in lung cancer cell lines” |
| Protein Expression | ”TP53 protein abundance in glioblastoma” |
Popular Queries
Oncogenes
Is MYC upregulated in breast cancer compared to normal?
Is EGFR expression higher in lung adenocarcinoma vs squamous?
What's the HER2 expression in HER2+ vs HER2- breast cancer?Tumor Suppressors
Is TP53 expression lower in tumors with TP53 mutations?
Compare BRCA1 expression in ovarian cancer vs normal tissue
Is RB1 downregulated in small cell lung cancer?Drug Targets
Does high ERBB2 expression predict survival in breast cancer?
Is BRAF mutated in melanoma?
What's the EGFR mutation rate in lung adenocarcinoma?Cancer-Specific Questions
# Kidney Cancer
Is VHL mutated in clear cell RCC?
Compare HIF1A expression between clear cell and papillary RCC
# Glioblastoma
What percentage of GBM has IDH1 mutations?
Does MGMT expression predict survival in glioblastoma?
# Breast Cancer
Is ESR1 expression different between ER+ and ER- tumors?
Does high Ki67 predict worse survival in breast cancer?Cell Line Queries (CCLE)
What is EGFR expression in lung cancer cell lines?
Which cell line sites have highest TP53 expression?
Is BRAF mutated in melanoma cell lines?Proteomics Queries (CPTAC)
What is TP53 protein abundance in glioblastoma?
Compare DDR1 protein levels across all CPTAC cancers
Is EGFR protein higher in lung adenocarcinoma?Pediatric Cancer Queries (TARGET)
What is MYC expression in neuroblastoma?
Compare TP53 expression in pediatric AML vs ALL
Is MYCN amplified in neuroblastoma?Tips for Writing Queries
Use specific TCGA cancer type codes for best results: LUAD (lung adenocarcinoma), BRCA (breast), GBM (glioblastoma), etc.
Be Specific
✅ “Is DDR1 higher in papillary RCC vs clear cell RCC?” ❌ “Is DDR1 higher in kidney cancer?”
Use Gene Symbols
✅ “TP53 mutation rate in colorectal cancer” ❌ “p53 mutations in colon cancer”
Specify Comparisons
✅ “Compare EGFR between LUAD and LUSC” ❌ “EGFR in lung cancer”