decoupler.get_dorothea

decoupler.get_dorothea(organism: str | int = 'human', levels: Literal['A', 'B', 'C', 'D'] | Iterable[Literal['A', 'B', 'C', 'D']] = ('A', 'B', 'C'), weight_dict: dict[str, int] | None = None, **kwargs) → DataFrame

DoRothEA gene regulatory network.

Wrapper to access DoRothEA gene regulatory network. DoRothEA is a comprehensive resource containing a curated collection of transcription factors (TFs) and their target genes. Each interaction is weighted by its mode of regulation (either positive or negative) and by its confidence level.

Parameters:

organismstr

The organism of interest: either NCBI Taxonomy ID, common name, latin name or Ensembl name. Organisms other than human will be translated from human data by orthology.

levelslist

List of confidence levels to return. Goes from A to D, A being the most confident and D being the less.

weight_dictdict

Dictionary of values to divide the mode of regulation (-1 or 1), one for each confidence level. Bigger values will generate weights close to zero.

kwargs

Passed to omnipath.interactions.Dorothea.get.

Returns:

doDataFrame

Dataframe in long format containing target genes for each TF with their associated weights and confidence level.