License Info

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Please check http://www.gnu.org/licenses/.

The code included in the present notebook is based on this script developed by Yusuke Hiki

Introduction

The present script takes the output of our Footprint-based analysis and matches the results againts the content of the Covid-19 Disease Maps

library(kableExtra)
library(stringr)

Results

Reading Input files

We first read the content ofthe Covid-19 Disease Maps which can be found in this file:

disease_map <- read.delim("https://gitlab.lcsb.uni.lu/covid/models/-/raw/master/Resources/Expand%20the%20diagrams/COVID19_Disease_Map_bipartite_crosslinked.tsv")

We then read the output of our Footprint-based analyisis, namely CARNIVAL's output network. This file can be found here.

carnival_results <- readRDS("InputFiles/carnival_results_withprogeny.rds")
carnival_nodes_hgnc <- unique(c(carnival_results$weightedSIF[,"Node1"], carnival_results$weightedSIF[,"Node2"]))

Matching the results

We finally match all our genes from the carnival network with all the genes from the different pathways included in the COVID19 Disease maps.

matching_genes <- character()
matching_pathways <- character()

for (i in 1:nrow(disease_map)){
  
  if (!(is.na(disease_map$source_hgnc[i]))) {
    
    source_nodes <- 
      str_replace(unlist(strsplit(disease_map$source_hgnc[i], split = ";")), "HGNC_SYMBOL:", "")
    
  } else {
    source_nodes <- c()
  }
  
  if (!(is.na(disease_map$target_hgnc[i]))) {
    
    target_nodes <- 
      str_replace(unlist(strsplit(disease_map$target_hgnc[i], split = ";")), "HGNC_SYMBOL:", "")
    
  }  else {
    target_nodes <- c()
  }
  
  all_nodes <- unique(c(source_nodes, target_nodes))
  
  if (length(all_nodes)!= 0){
    current_matching_genes <- intersect(carnival_nodes_hgnc, all_nodes)
    
    if (length(current_matching_genes) != 0){
      
      current_matching_pathways <-  rep(disease_map$source_diagram[i], length(current_matching_genes))
      matching_genes <- c(matching_genes, current_matching_genes)
      matching_pathways <- c(matching_pathways, current_matching_pathways)
    }
    
  }
  
}

disease_map_hgnc_carnival_detected <- 
  data.frame(source_diagram = matching_pathways, hgnc_carnival=matching_genes) %>% 
  dplyr::distinct()

and We visualize the results.

disease_map_hgnc_carnival_detected %>% 
  kbl(col.names = c("Covid19 DM Diagram", "Carnival nodes")) %>% 
  kable_styling()
Covid19 DM Diagram Carnival nodes
C19DMap:Interferon 1 pathway IRF3
C19DMap:Interferon 1 pathway TBK1
C19DMap:Interferon 1 pathway IKBKE
C19DMap:TGFbeta signalling MAPK3
C19DMap:TGFbeta signalling SMAD1
C19DMap:PAMP signalling TICAM1
C19DMap:PAMP signalling IKBKE
C19DMap:PAMP signalling IRF3
C19DMap:PAMP signalling TBK1
C19DMap:Pyrimidine deprivation IRF3
C19DMap:Pyrimidine deprivation TBK1
C19DMap:Orf3a protein interactions TICAM1
C19DMap:Endoplasmatic Reticulum stress ATF6
C19DMap:Endoplasmatic Reticulum stress ATF4
C19DMap:Endoplasmatic Reticulum stress MBTPS1
C19DMap:Interferon lambda pathway IRF3
C19DMap:Interferon lambda pathway TBK1 
write.table(x=disease_map_hgnc_carnival_detected, 
            file = "MatchingGenes/carnival_diagrams.tsv", sep = "\t",
            row.names = FALSE, quote = FALSE)

Session Info Details

## R version 4.0.4 (2021-02-15)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19042)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_Germany.1252  LC_CTYPE=English_Germany.1252   
## [3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C                    
## [5] LC_TIME=English_Germany.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.4.0    kableExtra_1.3.4
## 
## loaded via a namespace (and not attached):
##  [1] highr_0.9         bslib_0.2.5.1     compiler_4.0.4    pillar_1.7.0     
##  [5] jquerylib_0.1.4   tools_4.0.4       digest_0.6.27     tibble_3.1.6     
##  [9] jsonlite_1.7.2    evaluate_0.14     lifecycle_1.0.1   viridisLite_0.4.0
## [13] pkgconfig_2.0.3   rlang_1.0.1       DBI_1.1.2         cli_3.2.0        
## [17] rstudioapi_0.13   yaml_2.2.1        xfun_0.24         httr_1.4.2       
## [21] dplyr_1.0.8       xml2_1.3.2        knitr_1.33        generics_0.1.2   
## [25] sass_0.4.0        vctrs_0.3.8       systemfonts_1.0.2 tidyselect_1.1.2 
## [29] webshot_0.5.2     svglite_2.1.0     glue_1.4.2        R6_2.5.1         
## [33] fansi_1.0.2       rmarkdown_2.9     purrr_0.3.4       magrittr_2.0.1   
## [37] scales_1.1.1      htmltools_0.5.1.1 ellipsis_0.3.2    assertthat_0.2.1 
## [41] rvest_1.0.0       colorspace_2.0-1  utf8_1.2.2        stringi_1.6.2    
## [45] munsell_0.5.0     crayon_1.5.0