In sigven/oncoEnrichR: Cancer-dedicated gene set interpretation

Poorly characterized genes

The aim of this section is to highlight poorly characterized protein-coding genes or protein-coding genes with unknown function in the query set
A set of _uncharacterized/poorly characterized human protein-coding genes (n = r onc_enrich_report[['config']][['unknown_function']][['num_candidates']]) _ have been established based on
Gene names specifically designated with uncharacterized or open reading frame
Missing gene function summary in NCBI Gene AND function summary in UniProt Knowledgebase
Missing or limited (<= 2) gene ontology (GO) annotations with respect to molecular function (MF) or biological process (BP)
- Ontology annotations attributed with an electronic annotation evidence code (IEA) are not considered in this calculation (less reliable due to lack of manually review)
Query genes found within the set of poorly characterized protein-coding genes are listed below, colored in varying shades of red according to the level of missing characterization (from unknown function to poorly defined function )

show_ufunction_genes <- FALSE

if(nrow(onc_enrich_report[['data']][['unknown_function']][['hits_df']]) > 0){
  show_ufunction_genes <- TRUE
}

targets_unknown_function <- crosstalk::SharedData$new(
  onc_enrich_report[['data']][['unknown_function']][['hits_df']] |>
    dplyr::rename(go_terms = go_term_link))

crosstalk::bscols(
  list(
    crosstalk::filter_select("symbol", "Target", targets_unknown_function, ~symbol),
    crosstalk::filter_checkbox("has_gene_summary", "Has gene summary", targets_unknown_function, ~has_gene_summary)
  ),
  list(
    crosstalk::filter_slider("num_go_annotations", "Number of annotated GO terms (non-IEA)", targets_unknown_function, ~num_go_terms)
  )
)

htmltools::br()
DT::datatable(targets_unknown_function, 
              escape = F, 
              extensions=c("Buttons","Responsive"), 
              width = "100%",
              options=list(buttons = c('csv','excel'), 
                           dom = 'Bfrtip')) |>

  DT::formatStyle(
    "symbol",
    "unknown_function_rank", 
    color = "white",
    backgroundColor = DT::styleEqual(
      onc_enrich_report[["config"]][["unknown_function"]][["rank"]],
      onc_enrich_report[["config"]][["unknown_function"]][["colors"]]
    )
  )

cat('\n <ul><li>  <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white">&nbsp;&nbsp;<b>NO</b> genes with unknown or poorly defined functions were detected in the query set.&nbsp;&nbsp; </span></i></li></ul>',sep='\n')
cat('\n')
cat('<br><br>')