getLigandsReceptors: Retrieve a database of ligand-receptor pairs

In veltenlab/rnamagnet: Infers physical and signaling interactions from single-cell RNA-seq data

Description

Retrieve a database of ligand-receptor pairs

Usage

getLigandsReceptors(version = "latest",
  cellularCompartment = c("Membrane", "ECM", "Both", "Secreted"),
  manualAnnotation = "Correct", ligandClass = c("Other", "Cytokine",
  "Chemokine", "GrowthFactor", "Interleukin"))

Arguments

version	Currently supports the following values: latest points to 2.1.0 1.0.0 contains manual annotation for all genes expressed in bone marrow. This version was used for analysis is the Baccin et al paper. Information on heterodimeric receptors is only included for integrins. 2.0.0 contains manual annotation for all genes in the geneome (not yet complete). 2.1.0 integrates heterodimer information for non-integrin receptors from cellphoneDB. 3.0.0 adds a translation of the complete cellphoneDB to mouse homologues (not tested). Alternatively, a data frame with the same column names as ligandsReceptors_1.0.0 can be used.
cellularCompartment	A character vector to select permitted localizations of the ligand. Valid entries are Membrane, ECM, Secreted and Both, which refers to membrane-bound ligands that can also be secreted.
manualAnnotation	A character vector to select permitted annotation status of the interaction. Valid entries are Correct, Incorrect, Not Expressed (i.e. entries not annotated in v1.0.0) and Irrelevant (i.e. entries we consider correct but not relevant at homeostasis, e.g. interactions involving activated components of the complement system)
ligandClass	A character vector to select permitted classes of ligands. Defaults to all, i.e. c("Other","Cytokine","Chemokine","GrowthFactor","Interleukin")

Value

Returns a data frame with 11 columns:

• Pair.NameUnique identifier for the ligand-receptor pair

• Ligand.MouseMGI symbol of the ligand.

• Receptor.MouseMGI symbol of the receptor. In case multiple receptors are required for complex formation, multiple MGI symbols separated by &, as in Itgal&Itgb2.

• SourceRamilowski for entries taken from Ramilowski et al., Nature Communications 2015; Baccin for entries added as part of this work

• ReferencePubmed ID or similar

• ManualAnnotationThe literature evidence for all entries from Ramilowski et al with expression in bone where checked manually.

• Ligand.CCCellular Compartment of the ligand - one of Secreted, Membrane, Both, or ECM. Annotation is based on Gene Ontology, but was checked manually for entries with expression in bone

• Ligand.GOClassification of the ligand by gene ontology into one of the following classes: GrowthFactor, Cytokine, Chemokine, Interleukin, or Other

veltenlab/rnamagnet documentation built on June 24, 2021, 6:19 p.m.