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Human-Specific Heterogeneous Network

tkoi_net.Rd

An igraph object representing a human-specific heterogeneous biological network.

Usage

tkoi_net

Format

An igraph object where nodes and edges represent biological entities and their interactions. The node types included are:

Anatomy

Nodes representing anatomical structures and systems.

BiologicalProcess

Nodes for functional biological processes, such as signaling pathways.

CellType

Nodes describing different cell types.

CellularComponent

Nodes for subcellular structures, organelles, and macromolecular complexes.

ClinicalLab

Nodes representing clinical measurements and diagnostic data.

Complex

Nodes for molecular and protein complexes.

Compound

Nodes for endogenous metabolites in human.

Disease

Nodes for diseases and pathological conditions.

EC

Nodes categorized by Enzyme Commission numbers.

Gene

Nodes for genetic elements, such as genes and genetic markers.

MiRNA

Nodes for microRNAs and their regulatory roles.

MolecularFunction

Nodes describing molecular activities performed by gene products.

Pathway

Nodes representing sequences of molecular interactions and reactions.

Protein

Nodes for protein molecules.

ProteinDomain

Nodes for specific structural or functional domains within proteins.

ProteinFamily

Nodes for groups of evolutionarily related proteins.

PwGroup

Nodes for pathway groups aggregating multiple related pathways.

Reaction

Nodes for biochemical reactions and their participants.

Details

This heterogeneous network integrates multiple biological datasets to represent complex relationships within the human system. It serves as the foundation for network-based analyses in the tkoi package, such as personalized PageRank calculations and enrichment analyses.

Examples

data(tkoi_net)
igraph::summary(tkoi_net)
#> Error: 'summary' is not an exported object from 'namespace:igraph'
igraph::V(tkoi_net)$name[1:10]
#>  [1] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:0" 
#>  [2] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:1" 
#>  [3] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:2" 
#>  [4] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:3" 
#>  [5] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:4" 
#>  [6] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:5" 
#>  [7] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:6" 
#>  [8] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:8" 
#>  [9] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:10"
#> [10] "4:c77f6410-bc08-43ba-a172-0503ab1c93db:11"
igraph::E(tkoi_net)[1:10]
#> + 10/10622200 edges from 2542050 (vertex names):
#> [1] 4:c77f6410-bc08-43ba-a172-0503ab1c93db:0--4:c77f6410-bc08-43ba-a172-0503ab1c93db:3761 
#> [2] 4:c77f6410-bc08-43ba-a172-0503ab1c93db:0--4:c77f6410-bc08-43ba-a172-0503ab1c93db:7417 
#> [3] 4:c77f6410-bc08-43ba-a172-0503ab1c93db:1--4:c77f6410-bc08-43ba-a172-0503ab1c93db:6728 
#> [4] 4:c77f6410-bc08-43ba-a172-0503ab1c93db:1--4:c77f6410-bc08-43ba-a172-0503ab1c93db:7922 
#> [5] 4:c77f6410-bc08-43ba-a172-0503ab1c93db:1--4:c77f6410-bc08-43ba-a172-0503ab1c93db:12922
#> [6] 4:c77f6410-bc08-43ba-a172-0503ab1c93db:1--4:c77f6410-bc08-43ba-a172-0503ab1c93db:12660
#> [7] 4:c77f6410-bc08-43ba-a172-0503ab1c93db:2--4:c77f6410-bc08-43ba-a172-0503ab1c93db:7432 
#> [8] 4:c77f6410-bc08-43ba-a172-0503ab1c93db:2--4:c77f6410-bc08-43ba-a172-0503ab1c93db:11003
#> + ... omitted several edges