GeneFox

GeneFox explores public gene-expression and survival data from TCGA, NCBI GEO, GTEx, UCSC Xena, Treehouse, and CCLE. Statistics and visualizations run on your device; requests fetch only what your analysis needs.

Built for scientists who work with gene-expression data — no coding required.

WHAT YOU CAN DO

• Browse 65 supported TCGA/NCI Genomic Data Commons cohorts with case counts, sites, disease types, and demographics.
• Plot cohort gene expression as box, bar, or strip charts, stratified by clinical variables, subtype, sample type, or mutation status.
• Split any of those plots by a second variable for a side-by-side descriptive comparison; reported statistics stay with the single-variable view.
• Generate Kaplan–Meier curves with median summaries, log-rank p-values, and—where applicable—Cox High-vs-Low hazard ratios, 95% CIs, and proportional-hazards warnings.
• Compare tumor vs. adjacent-normal and matched GTEx normal tissue via the UCSC Xena TOIL hub, with effect sizes and Mann–Whitney U statistics.
• Explore 933 Treehouse CCLE v1 cell lines, grouped by TCGA acronym, tissue, disease, histology, or subtype.
• Browse independent pediatric and rare-tumor cohorts from UCSC Treehouse, drawn from studies outside TCGA and TARGET.
• Chart differential expression as an interactive volcano plot — expression or mutant-vs-wild-type contrasts — with panel-wise Benjamini–Hochberg FDR correction.
• Render gene-panel heatmaps with hierarchical clustering, annotation strips, Z-normalization, and an outlier-resistant color scale.
• Run Sample PCA (PC1/PC2) using up to 2,000 selected or top-variable genes, for GEO datasets and TCGA cohorts.
• Score custom signatures or 41 curated presets from MSigDB, Reactome, and WikiPathways, plus the Wagle et al. 2018 MPAS panel.
• Search NCBI GEO Series with cancer-term expansion. Supports series matrices, human NCBI-generated counts, complete-cohort ARCHS4 raw counts for GEO-classified human/mouse expression RNA-seq, and compatible supplementary matrices.
• Capture charts in Report Builder and export a multi-figure report with an auto-generated methods section.

ASK GENEFOX

Ask questions in plain language. Local interpretation runs first; optional Cloud Assist sends only its disclosed interpretation payload after one-time or standing consent. Scientific analyses stay on-device.

PRIVACY

GeneFox has no ads, behavioral-usage analytics, or third-party tracking. No GeneFox account is required. Bookmarks stay private and are portable via export/import.

DATA SOURCES

Consult each provider's site for the authoritative source:
• NCI Genomic Data Commons (TCGA and related programs): https://gdc.cancer.gov
• NCBI Gene Expression Omnibus (GEO): https://www.ncbi.nlm.nih.gov/geo/
• ARCHS4 fallback terms and citation: https://archs4.org/help
• GTEx Portal: https://gtexportal.org
• UCSC Xena: https://xenabrowser.net
• Treehouse Cell Line Compendium v1 (CCLE, July 2019): https://treehousegenomics.ucsc.edu/public-data-html/previous-compendia/
• Treehouse Tumor Compendium 25.01: https://treehousegenomics.ucsc.edu/public-data/

DISCLAIMER

GeneFox is an independent, nonclinical app for scientific research. It is NOT a government app and is not affiliated with or endorsed by any government entity or agency (including the U.S. NIH, NCI, or NCBI) or any data provider above. GeneFox is not a medical device and does not diagnose, treat, cure, or prevent any medical condition. Consult a qualified healthcare professional for medical advice, diagnosis, or treatment. Its outputs are not validated for clinical decision-making.

GeneFox is developed by Vindhya Data Science.