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Integrated Weighted Directed Networks for Prior Knowledge in Gene Regulation and Signaling

pkn.Rd

Two igraph objects representing integrated weighted directed networks: gr.graph describes transcription factor (TF) and target gene regulatory relationships, and sig.graph describes intra-cellular signaling interactions.

Usage

gr.graph

sig.graph

Format

Two igraph objects with directed and weighted edges, containing the following edge attributes:

weight

A numeric value representing the strength of the interaction.

consensus_stimulation

A logical attribute indicating whether the interaction is consistently recorded as stimulating across multiple databases in OmniPath.

consensus_inhibition

A logical attribute indicating whether the interaction is consistently recorded as inhibiting across multiple databases in OmniPath.

An object of class igraph of length 9867.

Source

OmniPath database via the OmniPathR package.

Details

These prior knowledge networks (PKN) are generated using the OmniPath R package and provide high-confidence regulatory and signaling interactions by integrating data from multiple databases. They are crucial for gene regulatory network (GRN) inference and upstream signaling pathway (USP) analysis in NNet.

Examples

# Summary of the gene regulatory network
summary(gr.graph)
#> IGRAPH 63bbc63 DNW- 6855 41206 -- 
#> + attr: name (v/c), weight (e/n), consensus_direction (e/n),
#> | consensus_stimulation (e/n), consensus_inhibition (e/n)

# Summary of the signaling network
summary(sig.graph)
#> IGRAPH 2d729a0 DNW- 9867 79242 -- 
#> + attr: name (v/c), weight (e/n), consensus_direction (e/n),
#> | consensus_stimulation (e/n), consensus_inhibition (e/n)

# Access edge attributes in gr.graph
edge_attr(gr.graph)
#> Error in edge_attr(gr.graph): could not find function "edge_attr"

# Access edge attributes in sig.graph
edge_attr(sig.graph)
#> Error in edge_attr(sig.graph): could not find function "edge_attr"