Cell-Cell Interaction Database
This page describes the automated construction of a cell-cell interaction database by filtering existing curated protein-protein interaction (PPI) data. Cell-cell interactions are important for understanding tissue organization. We and others have built cell-cell interaction databases (1,2,3,4,5). The resource available from this website represents an automatically built set of protein-protein interactions that can mediate cell-cell communication that is expanded compared to previous databases we have built.
Defining Receptor and Ligands
Receptor genes were defined based on the union of the annotations from
GO:0043235 - receptor complex,
GO:0008305 - integrin complex,
GO:0072657 - protein localized to membrane
GO:0043113 - receptor clustering
GO:0004872 - receptor activity,
GO:0009897 - external side of plasma membrane)
- search term -"Receptor [KW-0675]" go:0005886 organism:human.
This created a set of 4364 receptor genes (prior to manual curation)
Ligand genes were defined based on the union of the below annotations
GO:0005102 - receptor binding
the set of proteins labelled as secreted in the Secretome dataset (http://www.proteinatlas.org/humanproteome/secretome) (8).
This created a set of 3209 Ligand genes (prior to manual curation)
Extracellular Matrix (ECM) genes were defined based on the union of the annotations from
GO:0031012 - extracellular matrix
GO:0005578 - proteinacious extracellular matrix
GO:0005201 - extracellular matrix structural constituent
GO:1990430 - extracellular matrix protein binding
GO:0035426 - extracellular matrix cell signalling
This created a set of 433 ECM genes (prior to manual curation)
ECM, Receptor and ligand lists were manually curated
- genes that were neither receptors or ligands were removed
- misclassified genes were moved to the correct list (i.e. receptors found on the ligand list or vice versa)
After curation, the resulting ligand, receptor and ECM sets consisted of:
- Receptors - 1851 genes
- Ligands - 1593 genes
- ECM - 433 genes
In each of the above sets there are genes that are part of other sets (e.g. a gene can be ECM and ligand at the same time)
The set of protein interactions were downloaded from:
The entire interaction set was filtered to only include interactions that contained receptor-ligand, receptor-receptor, ligand-ligand, receptor-ecm, ligand-ecm or ecm-ecm interactions where the receptor, ligands and ecm were defined by the above lists.
The resulting Receptor-Ligand network contained 2,593 unique proteins and 38,446 unique interactions (115,900 interaction total)
Molecule Definition files
Ligands - table of ligands. (contains HGNC symbol and classification (Ligand, Ligand/ECM, Ligand/Receptor, Ligand/ECM/Receptor)
Receptors - table of receptors. (contains HGNC symbol and classification (Receptor, Receptor/ECM, Ligand/Receptor, Ligand/ECM/Receptor)
ECM - table of ECM. (contains HGNC symbol and classification (ECM, ECM/Receptor, ECM/Ligand, Ligand/ECM/Receptor)
Protein types - table of unique set of receptor, ligand and ECM genes (contains HGNC symbol as well as classification (Receptor, Ligand, ECM, ECM/Receptor, ECM/Ligand, Receptor/Ligand, Ligand/ECM/Receptor)
Version 1.0 - Built April 25, 2017 and contains iRefIndex version 14, Pathway Commons version 8 and BioGRID version 3.4.147
Ligand - Receptor interaction set - tab delimited file in mitab 2.5 format containing the following columns: (For people having issues unzipping the file on windows try - alternate file compatible with windows )
AliasA - main Alias for molecule A (often the recognized gene symbol)
AliasB- main Alias for molecule B (often the recognized gene symbol)
uidA - unique identifier for molecule A (depending on the source database this can be one of the following types uniprot, refseq, entrez gene id, ensembl)
uidB - unique identifier for molecule A (depending on the source database this can be one of the following types uniprot, refseq, entrez gene id, ensembl)
altA - list of alternate identifiers for molecule A.
altB - list of alternate identifiers for molecule B.
aliasA - list of alternate aliases for molecule A.
aliasB - list of alternate aliases for molecule B.
method - list of psi-mi terms indicating experimental methods used to discover interaction.
author - text listing authors
pmids - list of pmids associated with the interaction.
taxa - taxon id for molecule A.
taxb - taxon id for molecule B.
interactionType - list of psi-mi terms indicating the type of interactions it is.
sourcedb - source database.
interactionIdentifier - source database interaction identifier
confidence - confidence of interaction as supplied by database source
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