psite_annotation.addPSPKinaseSubstrateAnnotations

psite_annotation.addPSPKinaseSubstrateAnnotations(df, phosphoSitePlusKinaseSubstrateFile, gene_name=False, organism='human')

Annotate pandas dataframe with upstream kinases according to PhosphositePlus.

Adds the following annotation columns to dataframe:

  • PSP Kinases = all phosphorylating kinases according to PhosphoSitePlus, no distinction is made between in vivo and in vitro evidence (this can be added in the future, if necessary)

Example

df = pa.addPeptideAndPsitePositions(df, pa.pspFastaFile, pspInput = True)
df = pa.addPSPKinaseSubstrateAnnotations(df, pa.pspKinaseSubstrateFile)
Required columns:

Site positions

Parameters:

  • df (DataFrame) – pandas dataframe with ‘Site positions’ column

  • phosphoSitePlusKinaseSubstrateFile (str) – tab separated file with PhosphositePlus kinase substrate relations

  • gene_name (bool) – set to True to output the gene names instead of the kinase names

Returns:

annotated dataframe

Return type:

pd.DataFrame