Here we show how members of the query set that are involved in known protein complexes, using two different collections of protein complex annotations:
OmniPath - a meta-database of molecular biology prior knowledge, containing protein complex annotations predominantly from CORUM, ComplexPortal, Compleat
Human Protein Complex Map - hu.MAP v2.0 - created through an integration of > 15,000 proteomics experiments (biochemical fractionation data, proximity labeling data, and RNA hairpin pulldown data)
The protein complexes that overlap with members of the query set are ranked according to the mean cancer-relevance score of the participating members, and is color-coded in varying shades of blue (i.e. from low cancer-relevance to strong cancer-relevance ).
active_tab <- list() for(cl in c('omnipath','humap2')){ active_tab[[cl]] <- F } if(NROW(onc_enrich_report[['data']][['protein_complex']][['omnipath']]) > 0){ active_tab[['omnipath']] <- T }else{ if(NROW(onc_enrich_report[['data']][['protein_complex']][['humap2']]) > 0){ active_tab[['humap2']] <- T }else{ active_tab[['omnipath']] <- T } }
if(active_tab[['omnipath']] == T){ cat("") cat("#### OmniPath {.active}") cat("") }else{ cat("") cat("#### OmniPath") cat("") }
htmltools::br() stepsize <- 1 max_complex_members <- max(onc_enrich_report[['data']][['protein_complex']][['omnipath']]$num_target_members) if(max_complex_members > 10){ stepsize <- 2 } if(max_complex_members > 20){ stepsize <- 3 } omnipath_complexes_df <- crosstalk::SharedData$new(onc_enrich_report[['data']][['protein_complex']][['omnipath']]) crosstalk::bscols( list( crosstalk::filter_slider("num_target_members", "Minimum number of query set members in complex", omnipath_complexes_df, ~num_target_members, step = stepsize) ) ) htmltools::br() DT::datatable(omnipath_complexes_df, escape = F, extensions=c("Buttons","Responsive"), width = "100%", style = 'bootstrap', rownames = F, options=list(buttons = c('csv','excel'), pageLength = 10, bPaginate = T, dom = 'Bfrtip')) |> DT::formatStyle("complex_name", "complex_cancer_rank_score", color = "white", backgroundColor = DT::styleInterval( onc_enrich_report[['config']][['complex']][['breaks']], onc_enrich_report[['config']][['complex']][['colors']]) )
cat('<br><br>\n <ul><li> <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white"> <b>NO GENES</b> in the query set associate with protein complexes found in the OmniPath database . </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
if(active_tab[['humap2']] == T){ cat("") cat("#### hu.MAP v2.0 {.active}") cat("") }else{ cat("") cat("#### hu.MAP v2.0") cat("") }
htmltools::br() humap2_complexes_df <- crosstalk::SharedData$new(onc_enrich_report[['data']][['protein_complex']][['humap2']]) crosstalk::bscols( list( crosstalk::filter_slider("num_target_members", "Number of query set members in complex", humap2_complexes_df, ~num_target_members) ) ) htmltools::br() DT::datatable(humap2_complexes_df, escape = F, extensions=c("Buttons","Responsive"), width = "100%", style = 'bootstrap', rownames = F, options=list(buttons = c('csv','excel'), pageLength = 10, bPaginate = T, dom = 'Bfrtip')) |> DT::formatStyle("complex_name", "complex_cancer_rank_score", color = "white", backgroundColor = DT::styleInterval( onc_enrich_report[['config']][['complex']][['breaks']], onc_enrich_report[['config']][['complex']][['colors']]) )
cat('<br><br>\n <ul><li> <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white"> <b>NO GENES</b> in the query set associate with protein complexes established by the <b>hu.MAP v2.0</b> protein complex map . </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
Citation Note : If you use the output of the Protein complexes module of oncoEnrichR in your research, please cite the following resources and tools as appropriate:
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