Last updated: 2025-03-04

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📌 Overlap of GO functions between Corrmotif all and corrmotif Conc.

library(UpSetR)
library(dplyr)
library(tools)
library(GO.db)

# Set the folder path
folder_path <- "data/all_GO"

# Get a list of all CSV files in the folder
csv_files <- list.files(folder_path, pattern = "\\.csv$", full.names = TRUE)

# Loop through each file and assign it as a variable in the global environment
for (file in csv_files) {
  # Generate a valid R variable name from the file name (remove extension and replace spaces)
  file_name <- tools::file_path_sans_ext(basename(file))
  file_name <- gsub(" ", "_", file_name)  # Replace spaces with underscores
  file_name <- make.names(file_name)  # Ensure the name is valid in R
  
  # Assign the CSV file as a variable in the environment
  assign(file_name, read.csv(file, stringsAsFactors = FALSE))
}

# Define datasets (lists of Entrez Gene IDs)
sets <- list(
  "Non response all" = prob_all_1$ID,
  "CX_DOX shared late response all" = prob_all_2$ID,
  "Dox specific response all" = prob_all_3$ID,
  "Late high dose DOX specific response all" = prob_all_4$ID,
  
  "Non response (0.1)" = prob_1_0.1$ID,
  "DOX only mid-late (0.1)" = prob_2_0.1$ID,
  "CX_DOX mid-late (0.1)" = prob_3_0.1$ID,
  
  "Non response (0.5)" = prob_1_0.5$ID,
  "DOX only early-mid (0.5)" = prob_2_0.5$ID,
  "DOX only mid-late (0.5)" = prob_3_0.5$ID,
  "CX only mid-late (0.5)" = prob_4_0.5$ID,
  "CX_DOX mid-late (0.5)" = prob_5_0.5$ID
)

# Create a binary matrix for UpSet plot
all_genes <- unique(unlist(sets))  # Get all unique Entrez Gene IDs
binary_matrix <- data.frame(Gene_ID = all_genes)  # Initialize DataFrame

# Convert gene lists into a presence/absence matrix (1 = present, 0 = absent)
for (set_name in names(sets)) {
  binary_matrix[[set_name]] <- as.integer(all_genes %in% sets[[set_name]])
}

# Remove Gene_ID column as UpSetR only needs the binary matrix
binary_matrix <- binary_matrix[, -1]

upset(binary_matrix,
      sets = names(sets),
      order.by = "freq",
      sets.bar.color = "#56B4E9",  # Blue bars for set sizes
      mainbar.y.label = "Number of Shared Functions",
      sets.x.label = "GO terms per set",
      text.scale = 1.2,
      nintersects = 30)

Version Author Date
63ae929 sayanpaul01 2025-03-04

📌 Identify Unique GO Terms for Each Response Group

# Create a list to store unique GO terms per category
unique_go_terms <- list()

# Loop through each set to find unique GO terms
for (set_name in names(sets)) {
  # Get the GO terms for the current set
  current_go_terms <- sets[[set_name]]
  
  # Find GO terms that appear **only** in this set and not in others
  unique_terms <- current_go_terms[!(current_go_terms %in% unlist(sets[names(sets) != set_name]))]
  
  # Store in the list if there are any unique terms
  if (length(unique_terms) > 0) {
    unique_go_terms[[set_name]] <- unique_terms
  }
}

# Display unique GO terms for each category
unique_go_terms
$`Non response all`
[1] "GO:0071339" "GO:1990204" "GO:0101031" "GO:0070469" "GO:0070971"
[6] "GO:0044665"

$`CX_DOX shared late response all`
[1] "GO:0009132" "GO:0097421" "GO:0140719" "GO:0140299" "GO:0035064"
[6] "GO:0140034" "GO:1990498" "GO:0005682" "GO:0030532"

$`Dox specific response all`
[1] "GO:0045177" "GO:0016323" "GO:0009925"

$`Non response (0.1)`
 [1] "GO:0034470" "GO:0042254" "GO:0022613" "GO:0140053" "GO:0006413"
 [6] "GO:0006364" "GO:0032543" "GO:0048193" "GO:0033108" "GO:0016072"
[11] "GO:0008135" "GO:0090079" "GO:0030684" "GO:0005759" "GO:0098800"
[16] "GO:0098803" "GO:0010494" "GO:0000313" "GO:0005761" "GO:0035770"

$`DOX only mid-late (0.1)`
 [1] "GO:0009162" "GO:0009130" "GO:0006999" "GO:0006221" "GO:0007096"
 [6] "GO:0045859" "GO:0006978" "GO:0009129" "GO:0046785" "GO:0002562"
[11] "GO:0016444" "GO:0042772" "GO:0010458" "GO:0071900" "GO:0051292"
[16] "GO:0006289" "GO:0008584" "GO:0008406" "GO:0046546" "GO:0045739"
[21] "GO:0045137" "GO:0043549" "GO:0009124" "GO:0048144" "GO:0008301"
[26] "GO:0017056" "GO:0000803" "GO:0043240"

$`CX_DOX mid-late (0.1)`
[1] "GO:0005402"

$`DOX only early-mid (0.5)`
[1] "GO:0140297" "GO:0061629" "GO:0090575" "GO:0005667" "GO:0097550"
[6] "GO:0005669"

$`DOX only mid-late (0.5)`
 [1] "GO:0007186" "GO:0048738" "GO:0014706" "GO:0099084" "GO:0099173"
 [6] "GO:0045598" "GO:0046486" "GO:0003013" "GO:0045444" "GO:0046620"
[11] "GO:0016236"

$`CX only mid-late (0.5)`
 [1] "GO:0048599" "GO:0090305" "GO:0009994" "GO:2000243" "GO:0018105"
 [6] "GO:0018209" "GO:0035561" "GO:0090657" "GO:0048477" "GO:0071732"
[11] "GO:0006264" "GO:0000722" "GO:0071731" "GO:1902170" "GO:0004518"
[16] "GO:0019205"

$`CX_DOX mid-late (0.5)`
 [1] "GO:0048146" "GO:0030865" "GO:0051493" "GO:0051782" "GO:0090399"
 [6] "GO:2000279" "GO:0030010" "GO:1901875" "GO:0032147" "GO:0031398"
[11] "GO:0007163" "GO:0051972" "GO:0000235" "GO:0005818" "GO:0101019"

📌 Map GO IDs to Function Names Using GO.db

map_go_terms_local <- function(go_ids) {
  go_names <- unlist(mget(go_ids, GOTERM, ifnotfound = NA))  # Retrieve function names
  go_descriptions <- sapply(go_names, function(x) if (!is.na(x)) Term(x) else NA)
  
  # Create a dataframe
  go_mapping <- data.frame(GO_ID = go_ids, Function = go_descriptions, stringsAsFactors = FALSE)
  
  # Remove NAs (unrecognized GO IDs)
  go_mapping <- go_mapping[!is.na(go_mapping$Function), ]
  
  return(go_mapping)
}
mapped_unique_go_terms <- list()

for (set_name in names(unique_go_terms)) {
  if (length(unique_go_terms[[set_name]]) > 0) {
    go_data <- map_go_terms_local(unique_go_terms[[set_name]])
    mapped_unique_go_terms[[set_name]] <- go_data
  }
}
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# Display mapped GO terms
mapped_unique_go_terms
$`Non response all`
                GO_ID                          Function
GO:0071339 GO:0071339                      MLL1 complex
GO:1990204 GO:1990204            oxidoreductase complex
GO:0101031 GO:0101031 protein folding chaperone complex
GO:0070469 GO:0070469                       respirasome
GO:0070971 GO:0070971   endoplasmic reticulum exit site
GO:0044665 GO:0044665                    MLL1/2 complex

$`CX_DOX shared late response all`
                GO_ID                                 Function
GO:0009132 GO:0009132 nucleoside diphosphate metabolic process
GO:0097421 GO:0097421                       liver regeneration
GO:0140719 GO:0140719   constitutive heterochromatin formation
GO:0140299 GO:0140299           small molecule sensor activity
GO:0035064 GO:0035064               methylated histone binding
GO:0140034 GO:0140034    methylation-dependent protein binding
GO:1990498 GO:1990498              mitotic spindle microtubule
GO:0005682 GO:0005682                                 U5 snRNP
GO:0030532 GO:0030532  small nuclear ribonucleoprotein complex

$`Dox specific response all`
                GO_ID                    Function
GO:0045177 GO:0045177         apical part of cell
GO:0016323 GO:0016323 basolateral plasma membrane
GO:0009925 GO:0009925       basal plasma membrane

$`Non response (0.1)`
                GO_ID                                             Function
GO:0034470 GO:0034470                                     ncRNA processing
GO:0042254 GO:0042254                                  ribosome biogenesis
GO:0022613 GO:0022613                 ribonucleoprotein complex biogenesis
GO:0140053 GO:0140053                        mitochondrial gene expression
GO:0006413 GO:0006413                             translational initiation
GO:0006364 GO:0006364                                      rRNA processing
GO:0032543 GO:0032543                            mitochondrial translation
GO:0048193 GO:0048193                              Golgi vesicle transport
GO:0033108 GO:0033108     mitochondrial respiratory chain complex assembly
GO:0016072 GO:0016072                               rRNA metabolic process
GO:0008135 GO:0008135             translation factor activity, RNA binding
GO:0090079 GO:0090079 translation regulator activity, nucleic acid binding
GO:0030684 GO:0030684                                          preribosome
GO:0005759 GO:0005759                                 mitochondrial matrix
GO:0098800 GO:0098800         inner mitochondrial membrane protein complex
GO:0098803 GO:0098803                            respiratory chain complex
GO:0010494 GO:0010494                           cytoplasmic stress granule
GO:0000313 GO:0000313                                  organellar ribosome
GO:0005761 GO:0005761                               mitochondrial ribosome
GO:0035770 GO:0035770                            ribonucleoprotein granule

$`DOX only mid-late (0.1)`
                GO_ID
GO:0009162 GO:0009162
GO:0009130 GO:0009130
GO:0006999 GO:0006999
GO:0006221 GO:0006221
GO:0007096 GO:0007096
GO:0045859 GO:0045859
GO:0006978 GO:0006978
GO:0009129 GO:0009129
GO:0046785 GO:0046785
GO:0002562 GO:0002562
GO:0016444 GO:0016444
GO:0042772 GO:0042772
GO:0010458 GO:0010458
GO:0071900 GO:0071900
GO:0051292 GO:0051292
GO:0006289 GO:0006289
GO:0008584 GO:0008584
GO:0008406 GO:0008406
GO:0046546 GO:0046546
GO:0045739 GO:0045739
GO:0045137 GO:0045137
GO:0043549 GO:0043549
GO:0009124 GO:0009124
GO:0048144 GO:0048144
GO:0008301 GO:0008301
GO:0017056 GO:0017056
GO:0000803 GO:0000803
GO:0043240 GO:0043240
                                                                                                                  Function
GO:0009162                                                             deoxyribonucleoside monophosphate metabolic process
GO:0009130                                                        pyrimidine nucleoside monophosphate biosynthetic process
GO:0006999                                                                                       nuclear pore organization
GO:0006221                                                                      pyrimidine nucleotide biosynthetic process
GO:0007096                                                                                 regulation of exit from mitosis
GO:0045859                                                                           regulation of protein kinase activity
GO:0006978 DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
GO:0009129                                                           pyrimidine nucleoside monophosphate metabolic process
GO:0046785                                                                                      microtubule polymerization
GO:0002562                    somatic diversification of immune receptors via germline recombination within a single locus
GO:0016444                                                                                  somatic cell DNA recombination
GO:0042772                                             DNA damage response, signal transduction resulting in transcription
GO:0010458                                                                                               exit from mitosis
GO:0071900                                                          regulation of protein serine/threonine kinase activity
GO:0051292                                                                                   nuclear pore complex assembly
GO:0006289                                                                                      nucleotide-excision repair
GO:0008584                                                                                          male gonad development
GO:0008406                                                                                               gonad development
GO:0046546                                                              development of primary male sexual characteristics
GO:0045739                                                                               positive regulation of DNA repair
GO:0045137                                                                   development of primary sexual characteristics
GO:0043549                                                                                   regulation of kinase activity
GO:0009124                                                                   nucleoside monophosphate biosynthetic process
GO:0048144                                                                                        fibroblast proliferation
GO:0008301                                                                                            DNA binding, bending
GO:0017056                                                                          structural constituent of nuclear pore
GO:0000803                                                                                                  sex chromosome
GO:0043240                                                                                 Fanconi anaemia nuclear complex

$`CX_DOX mid-late (0.1)`
                GO_ID                                          Function
GO:0005402 GO:0005402 carbohydrate:monoatomic cation symporter activity

$`DOX only early-mid (0.5)`
                GO_ID
GO:0140297 GO:0140297
GO:0061629 GO:0061629
GO:0090575 GO:0090575
GO:0005667 GO:0005667
GO:0097550 GO:0097550
GO:0005669 GO:0005669
                                                                      Function
GO:0140297                            DNA-binding transcription factor binding
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
GO:0090575                   RNA polymerase II transcription regulator complex
GO:0005667                                     transcription regulator complex
GO:0097550                                 transcription preinitiation complex
GO:0005669                                  transcription factor TFIID complex

$`DOX only mid-late (0.5)`
                GO_ID                                     Function
GO:0007186 GO:0007186 G protein-coupled receptor signaling pathway
GO:0048738 GO:0048738            cardiac muscle tissue development
GO:0014706 GO:0014706           striated muscle tissue development
GO:0099084 GO:0099084     postsynaptic specialization organization
GO:0099173 GO:0099173                     postsynapse organization
GO:0045598 GO:0045598       regulation of fat cell differentiation
GO:0046486 GO:0046486               glycerolipid metabolic process
GO:0003013 GO:0003013                   circulatory system process
GO:0045444 GO:0045444                     fat cell differentiation
GO:0046620 GO:0046620                   regulation of organ growth
GO:0016236 GO:0016236                               macroautophagy

$`CX only mid-late (0.5)`
                GO_ID                                       Function
GO:0048599 GO:0048599                             oocyte development
GO:0090305 GO:0090305    nucleic acid phosphodiester bond hydrolysis
GO:0009994 GO:0009994                         oocyte differentiation
GO:2000243 GO:2000243    positive regulation of reproductive process
GO:0018105 GO:0018105                peptidyl-serine phosphorylation
GO:0018209 GO:0018209                   peptidyl-serine modification
GO:0035561 GO:0035561                regulation of chromatin binding
GO:0090657 GO:0090657                     telomeric loop disassembly
GO:0048477 GO:0048477                                      oogenesis
GO:0071732 GO:0071732              cellular response to nitric oxide
GO:0006264 GO:0006264                  mitochondrial DNA replication
GO:0000722 GO:0000722         telomere maintenance via recombination
GO:0071731 GO:0071731                       response to nitric oxide
GO:1902170 GO:1902170 cellular response to reactive nitrogen species
GO:0004518 GO:0004518                              nuclease activity
GO:0019205 GO:0019205 nucleobase-containing compound kinase activity

$`CX_DOX mid-late (0.5)`
                GO_ID
GO:0048146 GO:0048146
GO:0030865 GO:0030865
GO:0051493 GO:0051493
GO:0051782 GO:0051782
GO:0090399 GO:0090399
GO:2000279 GO:2000279
GO:0030010 GO:0030010
GO:1901875 GO:1901875
GO:0032147 GO:0032147
GO:0031398 GO:0031398
GO:0007163 GO:0007163
GO:0051972 GO:0051972
GO:0000235 GO:0000235
GO:0005818 GO:0005818
GO:0101019 GO:0101019
                                                                 Function
GO:0048146                positive regulation of fibroblast proliferation
GO:0030865                             cortical cytoskeleton organization
GO:0051493                        regulation of cytoskeleton organization
GO:0051782                           negative regulation of cell division
GO:0090399                                         replicative senescence
GO:2000279                negative regulation of DNA biosynthetic process
GO:0030010                                 establishment of cell polarity
GO:1901875 positive regulation of post-translational protein modification
GO:0032147                          activation of protein kinase activity
GO:0031398                  positive regulation of protein ubiquitination
GO:0007163                  establishment or maintenance of cell polarity
GO:0051972                              regulation of telomerase activity
GO:0000235                                             astral microtubule
GO:0005818                                                          aster
GO:0101019                              nucleolar exosome (RNase complex)

sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats4    tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GO.db_3.18.0         AnnotationDbi_1.64.1 IRanges_2.36.0      
[4] S4Vectors_0.40.1     Biobase_2.62.0       BiocGenerics_0.48.1 
[7] dplyr_1.1.4          UpSetR_1.4.0        

loaded via a namespace (and not attached):
 [1] KEGGREST_1.42.0         gtable_0.3.6            xfun_0.50              
 [4] bslib_0.8.0             ggplot2_3.5.1           vctrs_0.6.5            
 [7] bitops_1.0-7            generics_0.1.3          tibble_3.2.1           
[10] RSQLite_2.3.3           blob_1.2.4              pkgconfig_2.0.3        
[13] lifecycle_1.0.4         GenomeInfoDbData_1.2.11 farver_2.1.2           
[16] compiler_4.3.0          stringr_1.5.1           git2r_0.35.0           
[19] Biostrings_2.70.1       munsell_0.5.1           httpuv_1.6.15          
[22] GenomeInfoDb_1.38.8     htmltools_0.5.8.1       sass_0.4.9             
[25] RCurl_1.98-1.13         yaml_2.3.10             later_1.3.2            
[28] pillar_1.10.1           crayon_1.5.3            jquerylib_0.1.4        
[31] whisker_0.4.1           cachem_1.0.8            tidyselect_1.2.1       
[34] digest_0.6.34           stringi_1.8.3           labeling_0.4.3         
[37] rprojroot_2.0.4         fastmap_1.1.1           grid_4.3.0             
[40] colorspace_2.1-0        cli_3.6.1               magrittr_2.0.3         
[43] withr_3.0.2             scales_1.3.0            promises_1.3.0         
[46] bit64_4.0.5             rmarkdown_2.29          XVector_0.42.0         
[49] httr_1.4.7              bit_4.0.5               gridExtra_2.3          
[52] workflowr_1.7.1         png_0.1-8               memoise_2.0.1          
[55] evaluate_1.0.3          knitr_1.49              rlang_1.1.3            
[58] Rcpp_1.0.12             glue_1.7.0              DBI_1.2.3              
[61] rstudioapi_0.17.1       jsonlite_1.8.9          R6_2.5.1               
[64] plyr_1.8.9              fs_1.6.3                zlibbioc_1.48.0