is a Knowledge Graph.
DoRothEA is a curated resource of transcription factor (TF) – target gene (regulon) interactions with confidence scoring, enabling inference of TF activity from gene expression data. It integrates literature-curated interactions and various experimental evidence (e.g. ChIP-seq, TF binding motifs, perturbation data) to build context-agnostic and confidence-stratified regulons for multiple species. Frequently used with PROGENy to estimate pathway and TF activities.
genomics, biological systems, biomedical
Warning: No license entered
Unknown
Unknown
Unknown
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| dorothea.graph | DoRothEA Regulon Graph | v1.0.0 | GraphProduct | ❔ | Core TF–target regulon knowledge grap... |
| dorothea.r-package | DoRothEA R Package | dorothea | ProcessProduct | http | R package containing regulon data and... |
| dorothea.docs | DoRothEA Documentation | dorothea.html | DocumentationProduct | http | Project documentation, usage examples... |
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| bioteque.embeddings | Bioteque Embeddings | embeddings | Product | ❔ | Network embeddings of the Bioteque gr... |
DoRothEA provides a curated, confidence-stratified collection of transcription factor (TF) to target gene interactions (regulons) across species. It aggregates multiple evidence sources (literature curation, ChIP-seq, in silico TF binding predictions, expression perturbation signatures) to support robust TF activity inference from transcriptomic data.
Often paired with PROGENy for complementary pathway and TF activity inference. Users subset regulons by confidence level (e.g., A–C) to balance coverage and specificity.
Please cite the 2019 Nature Communications paper and, where appropriate, the latest preprint/update.
Created: September 11, 2025 | Last modified: September 11, 2025