Expression Queries

Examples of differential expression and tumor vs normal analyses.

Differential Expression

Compare gene expression between two cancer types.

Basic Comparison


Is DDR1 expression higher in papillary RCC vs clear cell RCC?

What you’ll get:

Boxplot comparing DDR1 expression in KIRP vs KIRC
P-value from Wilcoxon rank-sum test
Fold change between groups
Sample sizes for each cancer type

Using TCGA Codes


Compare EGFR expression between LUAD and LUSC

TCGA cancer type codes work directly:

LUAD = Lung adenocarcinoma
LUSC = Lung squamous cell carcinoma

Subtype Comparisons


How does HER2 expression differ between ER+ and ER- breast cancer?

Subtype comparisons require that subtype annotations exist in TCGA clinical data.

More Examples


Is KRAS expression higher in pancreatic cancer vs normal pancreas?
Compare MYC levels between Burkitt lymphoma and DLBCL
Is PTEN expression different in prostate cancer subtypes?
What's the ALK expression in NSCLC vs SCLC?

Tumor vs Normal

Compare gene expression in tumor tissue versus normal tissue.

Basic Tumor vs Normal


Is TP53 upregulated in breast cancer compared to normal?

What you’ll get:

Grouped boxplot (Tumor vs Normal)
P-value for the comparison
Fold change (tumor / normal)
Sample sizes

Fold Change Queries


What's the fold change of BRCA1 in ovarian tumors vs normal?

Returns the specific fold change value prominently.

Overexpression Queries


Is MYC overexpressed in liver cancer?
Is EGFR upregulated in glioblastoma?

These questions compare tumor samples to normal tissue.

Downregulation Queries


Is RB1 downregulated in small cell lung cancer?
Is CDKN2A expression lower in melanoma vs normal skin?

Normal tissue comes from TCGA matched normal samples when available, supplemented by GTEx data.

More Examples


Is VEGFA upregulated in renal cell carcinoma?
Compare BCL2 expression in lymphoma vs normal lymph nodes
Is CDK4 overexpressed in liposarcoma?
What's the difference in ERBB2 between HER2+ breast cancer and normal?

Multiple Gene Queries

Currently, BioQuery supports one gene per query. Run separate queries for multiple genes.

To analyze multiple genes:

Run individual queries for each gene
Use the API for batch processing
Export JSON for combined analysis

Common Patterns

Research Question → BioQuery

Research Question	BioQuery Query
”Is gene X a biomarker for cancer Y?"	"Is [gene] upregulated in [cancer]?"
"Does gene X differ between subtypes?"	"Compare [gene] between [subtype1] and [subtype2]"
"Is gene X a therapeutic target?"	"Is [gene] overexpressed in [cancer] vs normal?”

Cancer-Specific Queries

Breast Cancer:


Is ESR1 higher in ER+ vs ER- breast cancer?
Compare ERBB2 expression in HER2+ vs HER2- tumors
Is PGR expression associated with ER status?

Lung Cancer:


Is EGFR expression different between LUAD and LUSC?
Compare ALK expression in ALK+ vs ALK- NSCLC
Is KRAS higher in smokers vs never-smokers?

Colorectal Cancer:


Is APC expression lower in colorectal tumors vs normal?
Compare BRAF expression in MSI-H vs MSS tumors
Is KRAS upregulated in colorectal adenocarcinoma?