Table 2.
Resources of TF–gene interactions used in CollecTRI
| Database | Content extracted for compilation | Reference |
|---|---|---|
| ExTRI | All (cross-species) | Vazquez, 2022 (26) |
| TFactS | All (human, mouse, rat) | Essaghir, 2010 (53) |
| HTRIdb | All (human) | Bovolenta, 2012 (54) |
| IntAct | Subset: protein-gene interactions (human, mouse, rat) | Kerrien, 2012 (55) |
| GOA (updated) | Subset: protein-gene regulatory interactions (human, mouse, rat) | Huntley, 2015 (56) |
| TRRUST | All (human, mouse) | Han, 2015; Han, 2018 (24,57) |
| SIGNOR (updated) | Subset: interactions labeled with interaction mechanism ‘transcriptional regulation’ (human, mouse, rat) | Perfetto, 2016 (23) |
| CytReg | All (human, mouse) | CarrascoPro, 2019 (58) |
| GEREDB | Subset: interactions with regulator TFClass TF (human) | Huang, 2019 (59) |
| Pavlidis (new) | All (human, mouse) | Pavlidis, 2021 (34) |
| DoRothEA A (new) | All (human) | Garcia-Alonso, 2019 (15) |
| NTNU Curation (new) | Subset of about 20K sentences manually curated from ExTRI | Lægreid, in prep. |
The table indicates whether all interactions or subsets of them were included in CollecTRI.