Curated ligand-receptor interactions
Source:R/intercell_curated.R
curated_ligand_receptor_interactions.RdThe OmniPath intercell database annotates individual proteins and
complexes, and we combine these annotations with network interactions
on the client side, using import_intercell_network. The
architecture of this database is complex, aiming to cover a broad range
of knowledge on various levels of details and confidence. We can use the
intercell_consensus_filter and
filter_intercell_network functions for automated, data
driven quality filtering, in order to enrich the cell-cell communication
network in higher confidence interactions. However, for many users, a
simple combination of the most established, expert curated ligand-receptor
resources, provided by this function, fits better their purpose.
Usage
curated_ligand_receptor_interactions(
curated_resources = c("Guide2Pharma", "HPMR", "ICELLNET", "Kirouac2010", "CellTalkDB",
"CellChatDB", "connectomeDB2020"),
cellphonedb = TRUE,
cellinker = TRUE,
talklr = TRUE,
signalink = TRUE,
...
)Arguments
- curated_resources
Character vector of the resource names which are considered to be expert curated. You can include any post-translational network resource here, but if you include non ligand-receptor or non curated resources, the result will not fulfill the original intention of this function.
- cellphonedb
Logical: include the curated interactions from CellPhoneDB (not the whole CellPhoneDB but a subset of it).
- cellinker
Logical: include the curated interactions from Cellinker (not the whole Cellinker but a subset of it).
- talklr
Logical: include the curated interactions from talklr (not the whole talklr but a subset of it).
- signalink
Logical: include the ligand-receptor interactions from SignaLink. These are all expert curated.
- ...
Passed to
import_post_translational_interactions: further parameters for the interaction data. Should not contain `resources` argument as that would interfere with the downstream calls.
Value
A data frame similar to interactions (network) data frames, the source and target partners being ligand and receptor, respectively.
Details
Some resources are a mixture of curated and bulk imported interactions, and sometimes it's not trivial to separate these, we take care of these here. This function does not use the intercell database of OmniPath, but retrieves and filters a handful of network resources. The returned data frame has the layout of interactions (network) data frames, and the source and target partners implicitly correspond to ligand and receptor. The data frame shows all resources and references for all interactions, but each interaction is supported by at least one ligand-receptor resource which is supposed to based on expert curation in a ligand-receptor context.
Examples
lr <- curated_ligand_receptor_interactions()
lr
#> # A tibble: 6,307 × 15
#> source target source_genesymbol target_genesymbol is_directed is_stimulation
#> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 Q9GZX6 Q08334 IL22 IL10RB 1 1
#> 2 P01588 P19235 EPO EPOR 1 1
#> 3 Q9H2A7 O00574 CXCL16 CXCR6 1 1
#> 4 P21583 P10721 KITLG KIT 1 1
#> 5 Q07325 P49682 CXCL9 CXCR3 1 1
#> 6 P13501 P51681 CCL5 CCR5 1 1
#> 7 P80075 P51681 CCL8 CCR5 1 1
#> 8 P13236 P51681 CCL4 CCR5 1 1
#> 9 P05231 P40189 IL6 IL6ST 1 1
#> 10 P04083 P25090 ANXA1 FPR2 1 1
#> # ℹ 6,297 more rows
#> # ℹ 9 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
#> # references <chr>, curation_effort <dbl>, n_references <dbl>,
#> # n_resources <int>