ventolab / cellphonedb-data

20 stars 7 forks source link

CellphoneDB database

CellphoneDB database (aka cellphonedb-data) is a manually curated repository of receptors, ligands and their interactions.

The database can be used to search for a particular ligand/receptor or, in combination with the CellphoneDB tool, to interrogate your own single-cell transcriptomics data.

For more information, visit https://www.cellphonedb.org/ or our extended documentation

For CellphoneDB tool, visit https://github.com/ventolab/cellphonedb

Key features of CellphoneDB

Release notes

cellphonedb-data v5.0.0

1) New database (v5.0.0) with more manually curated interactions, making up to a total of 2,912 interactions. 2) Includes a new module (CellSign) containing Receptor-to-TF relationships retrieved by manual revision of the literature and are restricted to transcription factors with high specificity for an upstream receptor. CellSign database contains a total of 211 highly-specific direct receptor-to-TF relationships. CellSign uses TF activation as a downstream sensor for receptor activation upon cell-cell interaction, thus adding an extra layer of evidence to the likelihood of the cell-cell interaction. 3) New annotations of interactions as a result of manual curation, including: interactors, classification, directionality and modulatory effect.

cellphonedb-data v4.1.0

1) New database (v4.1.0) with more manually curated interactions, making up to a total of 2,923 interactions. 2) Non-curated exernal databases are discarded.

cellphonedb-data v4.0.0

1) More manually curated interactions added, with special focus on protein acting as heteromeric complexes. This version fo the database includes almost 2,000 high-confidence interactions, including heteromeric complexes! We believe modelling complexes is key to minimise false positives in the predictions. 2) Includes interactions involving non-proteins (i.e., not encoded by a gene) acting as ligands.

cellphonedb-data v3.0.0

1) Updated interactions involving WNT pathway.