Welcome to BioQuery
BioQuery lets you ask questions about cancer genomics in plain English and get publication-ready answers with interactive figures, statistical analysis, and reproducible methods.
What is BioQuery?
BioQuery is a natural language interface for exploring cancer genomics data from:
- TCGA - The Cancer Genome Atlas (33 cancer types, 11,000+ patients)
- GTEx - Genotype-Tissue Expression (normal tissue reference)
- TARGET - Pediatric cancers (7 cancer types, 6,000+ patients)
- CCLE - Cancer Cell Line Encyclopedia (~1,000 cell lines)
- CPTAC - Proteomics data (10 cancer types)
- GENIE - Real-world clinical genomics (~40,000 patients)
All data is queried via ISB-CGC BigQuery for fast, reproducible results.
Ask questions like:
- “Is DDR1 expression higher in papillary RCC vs clear cell RCC?”
- “Does high TP53 expression predict worse survival in lung cancer?”
- “What’s the BRAF mutation rate in melanoma?”
- “What’s DDR1 expression in lung cancer cell lines?”
- “What is TP53 protein abundance in glioblastoma?”
Key Features
Query Cards
Every query generates a Query Card - a reproducible, shareable analysis unit containing:
- Natural language question and interpretation
- Interactive Plotly figures
- Statistical results (p-values, effect sizes, confidence intervals)
- SQL query (for transparency)
- Grant-ready methods text
- Export options (PNG, SVG, JSON)
Analysis Types
| Analysis | Description | Example |
|---|---|---|
| Differential Expression | Compare gene expression between cancer types | ”Is EGFR higher in LUAD vs LUSC?” |
| Tumor vs Normal | Compare tumor to normal tissue | ”Is MYC upregulated in breast cancer?” |
| Mutation Frequency | Calculate mutation rates | ”What % of GBM has IDH1 mutations?” |
| Survival Analysis | Kaplan-Meier curves | ”Does high DDR1 predict worse survival?” |
| Cell Line Expression | Gene expression in CCLE cell lines | ”DDR1 expression in lung cancer cell lines” |
| Protein Expression | Protein abundance from CPTAC | ”TP53 protein levels in glioblastoma” |
Quick Start
- Go to bioquery.io/query
- Type a question in plain English
- Get your results - interactive figure + statistics
- Export - Download PNG/SVG for publications
BioQuery is currently in beta. Create a free account to get 2 queries per day, or contact us for expanded access.
Next Steps
- Quick Start Guide - Run your first query
- Understanding Results - Interpret your Query Card
- API Reference - Programmatic access
- Examples - Sample queries by analysis type