Sources & licences
Where the information shown in SCUBA comes from, and the licences it is used under.
Reference networks
The per-cell-type gene co-expression networks were built from single-cell data in the CZ CELLxGENE Discover Census (Chan Zuckerberg Initiative; data released under CC BY 4.0). CZI Single-Cell Biology Program et al., CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data. Nucleic Acids Research (2025).
Module annotation
Each module's title, category and written reasoning were generated by a large language model from the module's member genes, then reviewed and approved by a domain expert.
Gene annotation
| Source | Used for | Licence |
|---|---|---|
| Human Protein Atlas (version 25) | Gene identifiers, description, synonyms, chromosome position, predicted protein location, protein class | CC BY-SA 4.0 |
| Human Protein Atlas protein class "Essential proteins", from the DepMap Portal | Whether a gene is essential | CC BY-SA 4.0 (HPA); DepMap data CC BY 4.0 |
| UniProt | Protein function summaries; signal peptide and propeptide positions | CC BY 4.0 |
Protein structures
Predicted structures are models from the AlphaFold Protein Structure Database (Google DeepMind and EMBL-EBI, CC BY 4.0), displayed with iCn3D (NCBI).
External links
Gene pages link to the Human Protein Atlas and the Open Targets Platform.
Example datasets
- Pelka K. et al., Spatially organized multicellular immune hubs in human colorectal cancer. Cell (2021).
- COMBAT Consortium, A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell (2022).
- Thomas T. et al., A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease. Nature Immunology (2024).