Transcriptomic Knowledge Graph Integration with tKOI

Overview

tKOI (Transcriptomic Knowledge-graph Omics Integration) is an R package for integrating transcriptomic data with a biological knowledge graph to identify enriched biological concepts and pathways. It combines PageRank propagation with permutation testing and ontology-based annotations for high-resolution network interpretation.

Step-by-Step Example

This vignette demonstrates a complete workflow using the tkoi package.

Load Example Expression Data

file_path = system.file("extdata", "example_data.csv", package = "tkoi")
expression_data = data.table::fread(file_path)
head(expression_data)

Run tKOI Analysis

tkoi_result = run_tkoi(
  expression_data = expression_data,
  subnetwork = tkoi::tkoi_net,
  pvalue_threshold = 0.05,
  logfc_threshold = 0.25,
  indirect_link_threshold = 3,
  topology_similarity = 0.9,
  n_permutation = 100,
  damping_factor = 0.85,
  maximum_iteration = 500
)

Perform Gene Ontology Enrichment

tkoi_result = run_gene_enrichment(tkoi_result)

Visualize GO vs Graph Enrichment

tkoi_result@gene_enrichment_comparison$comparison_scatter1

tkoi_result@gene_enrichment_comparison$comparison_scatter2

Gene-Level Network Visualization

plt1 = make_gene_exploration_plot(
  tkoi_list = tkoi_result,
  sig_color = "#F39B7FB2",
  non_sig_color = "gray"
)
plt1

Export Enrichment Summary Table

gene_data = export_gene_exploration_data(tkoi_result)
head(gene_data)

Visualize Top Enriched Genes

plt2 = visualize_topn(
  tkoi_list = tkoi_result,
  category = "Gene",
  top_n = 25,
  high_color = "#FF5733",
  low_color = "#154360"
)
plt2

Save Analysis Result (Optional)

save(tkoi_result, file = "tkoi_result.rda")

Session Info

sessionInfo()
#> R version 4.5.0 (2025-04-11)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Sequoia 15.5
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> time zone: America/Los_Angeles
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.37     desc_1.4.3        R6_2.6.1          fastmap_1.2.0    
#>  [5] xfun_0.52         cachem_1.1.0      knitr_1.50        htmltools_0.5.8.1
#>  [9] rmarkdown_2.29    lifecycle_1.0.4   cli_3.6.5         sass_0.4.10      
#> [13] pkgdown_2.1.3     textshaping_1.0.1 jquerylib_0.1.4   systemfonts_1.2.3
#> [17] compiler_4.5.0    rstudioapi_0.17.1 tools_4.5.0       ragg_1.4.0       
#> [21] bslib_0.9.0       evaluate_1.0.4    yaml_2.3.10       jsonlite_2.0.0   
#> [25] rlang_1.1.6       fs_1.6.6          htmlwidgets_1.6.4

Wanjun Gu

2025-08-05