For PMID36828809 using DAVID2016 April

Loading libraries:

library("knitr")
library("kableExtra")
library("tidyverse")
library("stringr")
library("tidyr")
library("eulerr")
library("dplyr")

DAVID Results from the paper/web

getwd()
## [1] "/mnt/data/anusuiya/Projects/DAVID_reborn_tool/DAVID_vScripts"
DAVIDweb_results <- read.table("../output_lists/PMID36828809_output.txt", sep = "\t", header = TRUE) 

split_terms <- str_split(DAVIDweb_results$Term, pattern = "~")

DAVIDweb_results$GOID <- sapply(split_terms, "[", 1)
DAVIDweb_results$GO.Term <- sapply(split_terms, "[", 2)

DAVIDweb_results <- dplyr::select(DAVIDweb_results, GOID, GO.Term, Category, Count, X., PValue, Genes, List.Total, Pop.Hits, Pop.Total, Fold.Enrichment, Bonferroni, Benjamini, FDR)

tmp <- DAVIDweb_results
tmp$Genes=NULL

head(tmp,50) %>%      #Change PMID/PMCID
  kbl(caption="Top DAVID GO results from the the paper") %>%
  kable_paper("hover", full_width = F)
Top DAVID GO results from the the paper
GOID GO.Term Category Count X. PValue List.Total Pop.Hits Pop.Total Fold.Enrichment Bonferroni Benjamini FDR
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II GOTERM_BP_DIRECT 14 4.06 0.00e+00 304 20 19256 44.34 0.00e+00 0.00e+00 0.00e+00
GO:0019882 antigen processing and presentation GOTERM_BP_DIRECT 17 4.93 0.00e+00 304 47 19256 22.91 0.00e+00 0.00e+00 0.00e+00
GO:0002503 peptide antigen assembly with MHC class II protein complex GOTERM_BP_DIRECT 12 3.48 0.00e+00 304 16 19256 47.51 0.00e+00 0.00e+00 0.00e+00
GO:0002381 immunoglobulin production involved in immunoglobulin mediated immune response GOTERM_BP_DIRECT 12 3.48 0.00e+00 304 17 19256 44.71 0.00e+00 0.00e+00 0.00e+00
GO:0050870 positive regulation of T cell activation GOTERM_BP_DIRECT 13 3.77 0.00e+00 304 33 19256 24.95 0.00e+00 0.00e+00 0.00e+00
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II GOTERM_BP_DIRECT 12 3.48 0.00e+00 304 30 19256 25.34 0.00e+00 0.00e+00 0.00e+00
GO:0006955 immune response GOTERM_BP_DIRECT 32 9.28 0.00e+00 304 492 19256 4.12 1.00e-07 0.00e+00 0.00e+00
GO:0050852 T cell receptor signaling pathway GOTERM_BP_DIRECT 15 4.35 0.00e+00 304 112 19256 8.48 4.70e-06 6.00e-07 6.00e-07
GO:0002486 antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent GOTERM_BP_DIRECT 6 1.74 1.00e-07 304 8 19256 47.51 9.27e-05 1.03e-05 1.02e-05
GO:0001817 regulation of cytokine production GOTERM_BP_DIRECT 10 2.90 1.00e-07 304 50 19256 12.67 1.38e-04 1.38e-05 1.37e-05
GO:0001916 positive regulation of T cell mediated cytotoxicity GOTERM_BP_DIRECT 8 2.32 2.00e-07 304 27 19256 18.77 2.79e-04 2.53e-05 2.51e-05
GO:0032729 positive regulation of interferon-gamma production GOTERM_BP_DIRECT 11 3.19 4.00e-07 304 79 19256 8.82 8.17e-04 6.81e-05 6.75e-05
GO:0002250 adaptive immune response GOTERM_BP_DIRECT 23 6.67 3.00e-06 304 451 19256 3.23 1.00e-02 4.29e-04 4.25e-04
GO:0015739 sialic acid transport GOTERM_BP_DIRECT 4 1.16 3.77e-05 304 5 19256 50.67 7.00e-02 4.96e-03 4.92e-03
GO:0042102 positive regulation of T cell proliferation GOTERM_BP_DIRECT 8 2.32 7.11e-05 304 65 19256 7.80 1.20e-01 1.00e-02 1.00e-02
GO:0042270 protection from natural killer cell mediated cytotoxicity GOTERM_BP_DIRECT 4 1.16 7.45e-05 304 6 19256 42.23 1.30e-01 1.00e-02 1.00e-02
GO:0001819 positive regulation of cytokine production GOTERM_BP_DIRECT 8 2.32 7.84e-05 304 66 19256 7.68 1.30e-01 1.00e-02 1.00e-02
GO:0002729 positive regulation of natural killer cell cytokine production GOTERM_BP_DIRECT 4 1.16 2.04e-04 304 8 19256 31.67 3.10e-01 2.00e-02 2.00e-02
GO:0042613 MHC class II protein complex GOTERM_CC_DIRECT 15 4.35 0.00e+00 320 26 20472 36.91 0.00e+00 0.00e+00 0.00e+00
GO:0071556 integral component of lumenal side of endoplasmic reticulum membrane GOTERM_CC_DIRECT 15 4.35 0.00e+00 320 29 20472 33.09 0.00e+00 0.00e+00 0.00e+00
GO:0012507 ER to Golgi transport vesicle membrane GOTERM_CC_DIRECT 15 4.35 0.00e+00 320 56 20472 17.14 0.00e+00 0.00e+00 0.00e+00
GO:0030658 transport vesicle membrane GOTERM_CC_DIRECT 11 3.19 0.00e+00 320 41 20472 17.16 2.00e-07 0.00e+00 0.00e+00
GO:0009897 external side of plasma membrane GOTERM_CC_DIRECT 27 7.83 0.00e+00 320 456 20472 3.79 4.90e-06 1.00e-06 9.00e-07
GO:0042612 MHC class I protein complex GOTERM_CC_DIRECT 6 1.74 1.00e-07 320 9 20472 42.65 3.61e-05 6.00e-06 5.80e-06
GO:0030669 clathrin-coated endocytic vesicle membrane GOTERM_CC_DIRECT 10 2.90 1.40e-06 320 70 20472 9.14 4.63e-04 6.54e-05 6.25e-05
GO:0030666 endocytic vesicle membrane GOTERM_CC_DIRECT 10 2.90 1.50e-06 320 71 20472 9.01 5.23e-04 6.54e-05 6.25e-05
GO:0005765 lysosomal membrane GOTERM_CC_DIRECT 19 5.51 2.48e-05 320 373 20472 3.26 1.00e-02 9.33e-04 8.92e-04
GO:0010008 endosome membrane GOTERM_CC_DIRECT 15 4.35 4.65e-05 320 253 20472 3.79 2.00e-02 1.58e-03 1.51e-03
GO:0030670 phagocytic vesicle membrane GOTERM_CC_DIRECT 8 2.32 1.54e-04 320 74 20472 6.92 5.00e-02 4.74e-03 4.53e-03
GO:0032588 trans-Golgi network membrane GOTERM_CC_DIRECT 9 2.61 1.96e-04 320 102 20472 5.64 6.00e-02 1.00e-02 1.00e-02
GO:0005886 plasma membrane GOTERM_CC_DIRECT 107 31.01 3.71e-04 320 5066 20472 1.35 1.20e-01 1.00e-02 1.00e-02
GO:0005764 lysosome GOTERM_CC_DIRECT 15 4.35 3.76e-04 320 309 20472 3.11 1.20e-01 1.00e-02 1.00e-02
GO:0016020 membrane GOTERM_CC_DIRECT 62 17.97 3.87e-04 320 2547 20472 1.56 1.20e-01 1.00e-02 1.00e-02
GO:0009986 cell surface GOTERM_CC_DIRECT 22 6.38 1.11e-03 320 638 20472 2.21 3.10e-01 2.00e-02 2.00e-02
GO:0016021 integral component of membrane GOTERM_CC_DIRECT 110 31.88 1.21e-03 320 5406 20472 1.30 3.40e-01 2.00e-02 2.00e-02
GO:0032395 MHC class II receptor activity GOTERM_MF_DIRECT 11 3.19 0.00e+00 312 13 18811 51.02 0.00e+00 0.00e+00 0.00e+00
GO:0042605 peptide antigen binding GOTERM_MF_DIRECT 15 4.35 0.00e+00 312 37 18811 24.44 0.00e+00 0.00e+00 0.00e+00
GO:0023026 MHC class II protein complex binding GOTERM_MF_DIRECT 12 3.48 0.00e+00 312 27 18811 26.80 0.00e+00 0.00e+00 0.00e+00
GO:0005102 receptor binding GOTERM_MF_DIRECT 24 6.96 2.00e-07 312 396 18811 3.65 1.00e-04 2.51e-05 2.47e-05
GO:0015136 sialic acid transmembrane transporter activity GOTERM_MF_DIRECT 4 1.16 4.37e-05 312 5 18811 48.23 2.00e-02 4.27e-03 4.21e-03
GO:0030881 beta-2-microglobulin binding GOTERM_MF_DIRECT 4 1.16 2.36e-04 312 8 18811 30.15 1.10e-01 2.00e-02 2.00e-02
GO:0042608 T cell receptor binding GOTERM_MF_DIRECT 4 1.16 6.69e-04 312 11 18811 21.92 2.80e-01 5.00e-02 5.00e-02
GO:0046977 TAP binding GOTERM_MF_DIRECT 3 0.87 8.08e-04 312 3 18811 60.29 3.30e-01 5.00e-02 5.00e-02
GO:0005436 sodium:phosphate symporter activity GOTERM_MF_DIRECT 4 1.16 8.81e-04 312 12 18811 20.10 3.50e-01 5.00e-02 5.00e-02

DAVID Results from our R script/DAVID Reborn Tool:

script_results <- readRDS("ora_arranged2016.RDS")

script_results$GOID <- sapply(script_results$Description, function(term) strsplit(term, " ")[[1]][1])

script_results$GO.Term <- sapply(script_results$Description, function(term) paste(strsplit(term, " ")[[1]][-1], collapse = " "))

script_results <- dplyr::select(script_results, S_No, GOID, GO.Term, GeneRatio, BgRatio, pvalue, p.adjust, qvalue, geneID, Count, gr, br, EnrichmentScore)

# minimum of 2 genes
script_results <- subset(script_results,Count >=3 )

script_results <- subset(script_results,qvalue <= 0.638 )

tmp <- script_results
tmp$geneID=NULL

head(tmp,50) %>%
  kbl(caption="Top results from DAVID Reborn Tool") %>%
  kable_paper("hover", full_width = F)
Top results from DAVID Reborn Tool
S_No GOID GO.Term GeneRatio BgRatio pvalue p.adjust qvalue Count gr br EnrichmentScore
1 GO:0000786 CC nucleosome 29/353 61/19676 0.0000000 0.0000000 0.0000000 29 0.0821530 0.0031002 26.499048
2 GO:0071556 CC integral component of lumenal side of endoplasmic reticulum membrane 15/353 28/19676 0.0000000 0.0000000 0.0000000 15 0.0424929 0.0014231 29.860380
3 GO:0060333 BP interferon-gamma-mediated signaling pathway 20/353 77/19676 0.0000000 0.0000000 0.0000000 20 0.0566572 0.0039134 14.477760
4 GO:0042605 MF peptide antigen binding 15/353 35/19676 0.0000000 0.0000000 0.0000000 15 0.0424929 0.0017788 23.888304
5 GO:0042613 CC MHC class II protein complex 12/353 19/19676 0.0000000 0.0000000 0.0000000 12 0.0339943 0.0009656 35.203817
6 GO:0012507 CC ER to Golgi transport vesicle membrane 15/353 49/19676 0.0000000 0.0000000 0.0000000 15 0.0424929 0.0024903 17.063074
7 GO:0006334 BP nucleosome assembly 20/353 108/19676 0.0000000 0.0000000 0.0000000 20 0.0566572 0.0054889 10.322107
8 GO:0002504 BP antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 10/353 15/19676 0.0000000 0.0000000 0.0000000 10 0.0283286 0.0007624 37.159585
9 GO:0000788 CC nuclear nucleosome 12/353 27/19676 0.0000000 0.0000000 0.0000000 12 0.0339943 0.0013722 24.773056
10 GO:0032395 MF MHC class II receptor activity 8/353 11/19676 0.0000000 0.0000000 0.0000000 8 0.0226629 0.0005591 40.537729
11 GO:0030658 CC transport vesicle membrane 11/353 36/19676 0.0000000 0.0000000 0.0000000 11 0.0311615 0.0018296 17.031476
12 GO:0019221 BP cytokine-mediated signaling pathway 26/353 303/19676 0.0000000 0.0000000 0.0000000 26 0.0736544 0.0153995 4.782917
13 GO:0042612 CC MHC class I protein complex 7/353 11/19676 0.0000000 0.0000000 0.0000000 7 0.0198300 0.0005591 35.470512
14 GO:0046982 MF protein heterodimerization activity 29/353 446/19676 0.0000000 0.0000003 0.0000003 29 0.0821530 0.0226672 3.624309
15 GO:0006955 BP immune response 29/353 498/19676 0.0000000 0.0000031 0.0000029 29 0.0821530 0.0253100 3.245867
16 GO:0030669 CC clathrin-coated endocytic vesicle membrane 9/353 41/19676 0.0000000 0.0000036 0.0000033 9 0.0254958 0.0020838 12.235473
17 GO:0019886 BP antigen processing and presentation of exogenous peptide antigen via MHC class II 12/353 92/19676 0.0000001 0.0000085 0.0000078 12 0.0339943 0.0046757 7.270353
18 GO:0031295 BP T cell costimulation 11/353 78/19676 0.0000001 0.0000123 0.0000113 11 0.0311615 0.0039642 7.860681
19 GO:0030666 CC endocytic vesicle membrane 10/353 66/19676 0.0000003 0.0000213 0.0000197 10 0.0283286 0.0033543 8.445360
20 GO:0032588 CC trans-Golgi network membrane 9/353 51/19676 0.0000003 0.0000213 0.0000197 9 0.0254958 0.0025920 9.836361
21 GO:0060337 BP type I interferon signaling pathway 10/353 68/19676 0.0000004 0.0000262 0.0000241 10 0.0283286 0.0034560 8.196967
22 GO:0050852 BP T cell receptor signaling pathway 14/353 156/19676 0.0000009 0.0000609 0.0000562 14 0.0396601 0.0079284 5.002252
23 GO:0002479 BP antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent 10/353 75/19676 0.0000009 0.0000609 0.0000562 10 0.0283286 0.0038118 7.431917
24 GO:0006325 BP chromatin organization 16/353 211/19676 0.0000014 0.0000914 0.0000843 16 0.0453258 0.0107237 4.226683
25 GO:0042590 BP antigen processing and presentation of exogenous peptide antigen via MHC class I 10/353 79/19676 0.0000015 0.0000914 0.0000843 10 0.0283286 0.0040150 7.055617
26 GO:0002474 BP antigen processing and presentation of peptide antigen via MHC class I 11/353 99/19676 0.0000016 0.0000983 0.0000907 11 0.0311615 0.0050315 6.193264
27 GO:0001819 BP positive regulation of cytokine production 6/353 24/19676 0.0000033 0.0001896 0.0001750 6 0.0169972 0.0012198 13.934844
28 GO:0006342 BP chromatin silencing 7/353 38/19676 0.0000044 0.0002377 0.0002194 7 0.0198300 0.0019313 10.267780
29 GO:0019882 BP antigen processing and presentation 7/353 38/19676 0.0000044 0.0002377 0.0002194 7 0.0198300 0.0019313 10.267780
30 GO:0023026 MF MHC class II protein complex binding 5/353 16/19676 0.0000067 0.0003497 0.0003226 5 0.0141643 0.0008132 17.418555
31 GO:0042102 BP positive regulation of T cell proliferation 8/353 58/19676 0.0000087 0.0004387 0.0004048 8 0.0226629 0.0029478 7.688190
32 GO:0005765 CC lysosomal membrane 16/353 257/19676 0.0000177 0.0008632 0.0007965 16 0.0453258 0.0130616 3.470156
33 GO:0050830 BP defense response to Gram-positive bacterium 8/353 66/19676 0.0000230 0.0010903 0.0010060 8 0.0226629 0.0033543 6.756288
34 GO:0030881 MF beta-2-microglobulin binding 4/353 11/19676 0.0000304 0.0013995 0.0012914 4 0.0113314 0.0005591 20.268864
35 GO:0019731 BP antibacterial humoral response 6/353 39/19676 0.0000632 0.0028261 0.0026077 6 0.0169972 0.0019821 8.575289
36 GO:0032729 BP positive regulation of interferon-gamma production 6/353 45/19676 0.0001442 0.0062427 0.0057604 6 0.0169972 0.0022871 7.431917
37 GO:0070062 CC extracellular exosome 75/353 2774/19676 0.0001477 0.0062427 0.0057604 75 0.2124646 0.1409839 1.507013
38 GO:0003677 MF DNA binding 49/353 1597/19676 0.0001521 0.0062601 0.0057764 49 0.1388102 0.0811649 1.710225
39 GO:0035435 BP phosphate ion transmembrane transport 4/353 16/19676 0.0001563 0.0062670 0.0057828 4 0.0113314 0.0008132 13.934844
40 GO:0000790 CC nuclear chromatin 11/353 168/19676 0.0002335 0.0091316 0.0084261 11 0.0311615 0.0085383 3.649602
41 GO:0001618 MF virus receptor activity 7/353 70/19676 0.0002562 0.0097724 0.0090174 7 0.0198300 0.0035576 5.573938
42 GO:0002227 BP innate immune response in mucosa 4/353 19/19676 0.0003189 0.0118768 0.0109592 4 0.0113314 0.0009656 11.734606
43 GO:0009986 CC cell surface 22/353 544/19676 0.0003595 0.0130774 0.0120669 22 0.0623229 0.0276479 2.254166
44 GO:0030670 CC phagocytic vesicle membrane 6/353 55/19676 0.0004417 0.0156994 0.0144863 6 0.0169972 0.0027953 6.080659
45 GO:0030261 BP chromosome condensation 3/353 10/19676 0.0006256 0.0212721 0.0196285 3 0.0084986 0.0005082 16.721813
46 GO:0046415 BP urate metabolic process 3/353 10/19676 0.0006256 0.0212721 0.0196285 3 0.0084986 0.0005082 16.721813
47 GO:0005654 CC nucleoplasm 67/353 2554/19676 0.0008222 0.0273605 0.0252465 67 0.1898017 0.1298028 1.462231
48 GO:0016045 BP detection of bacterium 3/353 11/19676 0.0008489 0.0276587 0.0255216 3 0.0084986 0.0005591 15.201648
49 GO:0005102 MF receptor binding 16/353 362/19676 0.0008973 0.0286393 0.0264265 16 0.0453258 0.0183980 2.463619
50 GO:0030449 BP regulation of complement activation 4/353 26/19676 0.0011142 0.0342490 0.0316028 4 0.0113314 0.0013214 8.575289

Compare the genes that are recognised in both analyses

Extract the gene lists from the results of the web tool and the reborn tool to see where genes are being exluded.

web_genes <- unique(gsub(" ","",unlist(strsplit(DAVIDweb_results$Genes,","))))
#web_genes <- sort(web_genes)
filtered_genes <- web_genes[DAVIDweb_results$FDR < 0.05]
web_genes <- sort(unique(filtered_genes))
str(web_genes)
##  chr [1:169] "ABCF1" "ABHD16A" "AGER" "AGPAT1" "AIF1" "AMIGO3" "B3GALT4" ...
#481 genes

script_genes <- unique(unlist(strsplit(script_results$geneID," ")))
script_genes <- sort(script_genes)
str(script_genes)
##  chr [1:352] "ABCF1" "ABHD16A" "ABT1" "ACOT13" "ADAD1" "AGER" "AGPAT1" ...
# 499 genes looks right

v1 <- list("web"=web_genes,"script"=script_genes)

plot(euler(v1),quantities = list(cex = 1.0), labels = list(cex = 1.5))

message("Genes unique to web")
## Genes unique to web
setdiff(web_genes,script_genes)
## [1] "C6ORF136" "C6ORF47"  "CD226"    "IL2RA"    "KCNK17"   "MANBA"    "MMEL1"   
## [8] "SH2B3"
message("Genes unique to script")
## Genes unique to script
setdiff(script_genes, web_genes)
##   [1] "ABT1"            "ACOT13"          "ADAD1"           "ALDH5A1"        
##   [5] "AMT"             "ANKRD50"         "APEH"            "APOM"           
##   [9] "ARIH2"           "ATF6B"           "ATP6V1G2"        "ATP6V1G2-DDX39B"
##  [13] "ATRIP"           "BAD"             "BAK1"            "BBS12"          
##  [17] "BRD2"            "BTNL2"           "C2"              "C3orf62"        
##  [21] "C6orf10"         "C6orf136"        "C6orf15"         "C6orf25"        
##  [25] "C6orf47"         "C6orf62"         "CARF"            "CCDC36"         
##  [29] "CCHCR1"          "CCNA2"           "CD28"            "CDC25A"         
##  [33] "CHTF8"           "COL11A2"         "COL7A1"          "CYP21A2"        
##  [37] "DALRD3"          "DAXX"            "DCDC2"           "DDAH2"          
##  [41] "DDX39B"          "DPCR1"           "DYRK1A"          "EHMT2"          
##  [45] "ERCC4"           "ESRRA"           "FAM117B"         "FAM212A"        
##  [49] "FAM65B"          "FAM71F1"         "FGF2"            "FKBPL"          
##  [53] "GMNN"            "GMPPB"           "GPANK1"          "GPX1"           
##  [57] "GPX5"            "GPX6"            "GSPT1"           "GTF2H4"         
##  [61] "HEMK1"           "HIST1H1A"        "HIST1H1B"        "HIST1H1C"       
##  [65] "HIST1H1D"        "HIST1H1T"        "HIST1H2AA"       "HIST1H2AB"      
##  [69] "HIST1H2AC"       "HIST1H2AD"       "HIST1H2AG"       "HIST1H2AH"      
##  [73] "HIST1H2AJ"       "HIST1H2BA"       "HIST1H2BB"       "HIST1H2BC"      
##  [77] "HIST1H2BD"       "HIST1H2BH"       "HIST1H2BI"       "HIST1H2BJ"      
##  [81] "HIST1H2BK"       "HIST1H2BL"       "HIST1H2BM"       "HIST1H2BN"      
##  [85] "HIST1H2BO"       "HIST1H3A"        "HIST1H4A"        "HIST1H4G"       
##  [89] "HMGN4"           "IMPDH1"          "IP6K1"           "IP6K2"          
##  [93] "IRF5"            "KIAA1109"        "KLF14"           "KLHDC8B"        
##  [97] "LAMB2"           "LRRC16A"         "LSM2"            "MAPKAPK3"       
## [101] "MCCD1"           "MDC1"            "MON1A"           "MSH5"           
## [105] "MSH5-SAPCD1"     "MST1R"           "NCKIPSD"         "NDUFAF3"        
## [109] "NFKBIL1"         "NICN1"           "NME6"            "NRF1"           
## [113] "NUDT6"           "PBX2"            "PDF"             "PFKFB4"         
## [117] "PHF1"            "PMM2"            "POU5F1"          "PPP1R14B"       
## [121] "PPP1R18"         "PRKD2"           "PRM1"            "PRM2"           
## [125] "PRM3"            "PRMT7"           "PRSS16"          "PSMB9"          
## [129] "PSORS1C2"        "QARS"            "RASGRP2"         "RBM28"          
## [133] "RBM6"            "RING1"           "RMI2"            "RNF123"         
## [137] "RNF39"           "RPP21"           "RPS6KA4"         "RXRB"           
## [141] "SEMA3F"          "SFTA2"           "SKIV2L"          "SLC1A5"         
## [145] "SLC25A20"        "SPATA5"          "STK19"           "STRIP2"         
## [149] "TCF19"           "TDP2"            "TERF2"           "TEX40"          
## [153] "TNP2"            "TNPO3"           "TNXB"            "TRAIP"          
## [157] "TRIM10"          "TRIM26"          "TRIM31"          "TRIM38"         
## [161] "TRIM40"          "TRMT112"         "TUBB"            "TUSC2"          
## [165] "UBA7"            "UBD"             "UBE2H"           "UCN2"           
## [169] "UQCRC1"          "USP19"           "VARS"            "VARS2"          
## [173] "VWA7"            "WDR46"           "ZBTB12"          "ZFP57"          
## [177] "ZKSCAN3"         "ZKSCAN4"         "ZKSCAN8"         "ZMYND10"        
## [181] "ZNF165"          "ZNF184"          "ZNF311"          "ZNF322"         
## [185] "ZNF391"          "ZNF589"          "ZSCAN12"         "ZSCAN16"        
## [189] "ZSCAN23"         "ZSCAN31"         "ZSCAN9"

Comparing results from the web-server and our R script:

# From DAVID webserver table output: 
#web_split <- sapply(strsplit(PMID33947848_results$Term,"~"),"[[",1)

DAVID_webserver <- DAVIDweb_results %>% #Change PMID/PMCID
  select(GOID, Count, PValue, Fold.Enrichment, FDR)

DAVID_reborn <- script_results %>%
  select(S_No, GOID, GO.Term, GeneRatio, pvalue, p.adjust, Count ,EnrichmentScore)

comparison_table <- merge(DAVID_webserver, DAVID_reborn, by = "GOID", all = TRUE)

comparison_table <- comparison_table[order(comparison_table$PValue),]

comparison_table$geneID=NULL

head(comparison_table,50) %>%
  kbl(caption="Top replication results") %>%
  kable_paper("hover", full_width = F)
Top replication results
GOID Count.x PValue Fold.Enrichment FDR S_No GO.Term GeneRatio pvalue p.adjust Count.y EnrichmentScore
38 GO:0002504 14 0.00e+00 44.34 0.00e+00 8 BP antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 10/353 0.0000000 0.0000000 10 37.159585
251 GO:0042613 15 0.00e+00 36.91 0.00e+00 5 CC MHC class II protein complex 12/353 0.0000000 0.0000000 12 35.203817
316 GO:0071556 15 0.00e+00 33.09 0.00e+00 2 CC integral component of lumenal side of endoplasmic reticulum membrane 15/353 0.0000000 0.0000000 15 29.860380
183 GO:0019882 17 0.00e+00 22.91 0.00e+00 29 BP antigen processing and presentation 7/353 0.0000044 0.0002377 7 10.267780
37 GO:0002503 12 0.00e+00 47.51 0.00e+00 NA NA NA NA NA NA NA
33 GO:0002381 12 0.00e+00 44.71 0.00e+00 NA NA NA NA NA NA NA
220 GO:0032395 11 0.00e+00 51.02 0.00e+00 10 MF MHC class II receptor activity 8/353 0.0000000 0.0000000 8 40.537729
248 GO:0042605 15 0.00e+00 24.44 0.00e+00 4 MF peptide antigen binding 15/353 0.0000000 0.0000000 15 23.888304
292 GO:0050870 13 0.00e+00 24.95 0.00e+00 70 BP positive regulation of T cell activation 3/353 0.0038247 0.0854554 3 9.289896
157 GO:0012507 15 0.00e+00 17.14 0.00e+00 6 CC ER to Golgi transport vesicle membrane 15/353 0.0000000 0.0000000 15 17.063074
191 GO:0023026 12 0.00e+00 26.80 0.00e+00 30 MF MHC class II protein complex binding 5/353 0.0000067 0.0003497 5 17.418555
184 GO:0019886 12 0.00e+00 25.34 0.00e+00 17 BP antigen processing and presentation of exogenous peptide antigen via MHC class II 12/353 0.0000001 0.0000085 12 7.270353
115 GO:0006955 32 0.00e+00 4.12 0.00e+00 15 BP immune response 29/353 0.0000000 0.0000031 29 3.245867
203 GO:0030658 11 0.00e+00 17.16 0.00e+00 11 CC transport vesicle membrane 11/353 0.0000000 0.0000000 11 17.031476
291 GO:0050852 15 0.00e+00 8.48 6.00e-07 22 BP T cell receptor signaling pathway 14/353 0.0000009 0.0000609 14 5.002252
148 GO:0009897 27 0.00e+00 3.79 9.00e-07 807 CC external side of plasma membrane 5/353 0.3146044 0.5969064 5 1.346362
36 GO:0002486 6 1.00e-07 47.51 1.02e-05 NA NA NA NA NA NA NA
24 GO:0001817 10 1.00e-07 12.67 1.37e-05 NA NA NA NA NA NA NA
250 GO:0042612 6 1.00e-07 42.65 5.80e-06 13 CC MHC class I protein complex 7/353 0.0000000 0.0000000 7 35.470512
26 GO:0001916 8 2.00e-07 18.77 2.51e-05 54 BP positive regulation of T cell mediated cytotoxicity 3/353 0.0014326 0.0407391 3 12.862933
55 GO:0005102 24 2.00e-07 3.65 2.47e-05 49 MF receptor binding 16/353 0.0008973 0.0286393 16 2.463619
224 GO:0032729 11 4.00e-07 8.82 6.75e-05 36 BP positive regulation of interferon-gamma production 6/353 0.0001442 0.0062427 6 7.431917
205 GO:0030669 10 1.40e-06 9.14 6.25e-05 16 CC clathrin-coated endocytic vesicle membrane 9/353 0.0000000 0.0000036 9 12.235473
204 GO:0030666 10 1.50e-06 9.01 6.25e-05 19 CC endocytic vesicle membrane 10/353 0.0000003 0.0000213 10 8.445360
32 GO:0002250 23 3.00e-06 3.23 4.25e-04 93 BP adaptive immune response 7/353 0.0128242 0.2074553 7 2.807019
79 GO:0005765 19 2.48e-05 3.26 8.92e-04 32 CC lysosomal membrane 16/353 0.0000177 0.0008632 16 3.470156
159 GO:0015739 4 3.77e-05 50.67 4.92e-03 NA NA NA NA NA NA NA
158 GO:0015136 4 4.37e-05 48.23 4.21e-03 NA NA NA NA NA NA NA
150 GO:0010008 15 4.65e-05 3.79 1.51e-03 110 CC endosome membrane 8/353 0.0177282 0.2490753 8 2.436694
238 GO:0042102 8 7.11e-05 7.80 1.00e-02 31 BP positive regulation of T cell proliferation 8/353 0.0000087 0.0004387 8 7.688190
240 GO:0042270 4 7.45e-05 42.23 1.00e-02 NA NA NA NA NA NA NA
25 GO:0001819 8 7.84e-05 7.68 1.00e-02 27 BP positive regulation of cytokine production 6/353 0.0000033 0.0001896 6 13.934844
206 GO:0030670 8 1.54e-04 6.92 4.53e-03 44 CC phagocytic vesicle membrane 6/353 0.0004417 0.0156994 6 6.080659
223 GO:0032588 9 1.96e-04 5.64 1.00e-02 20 CC trans-Golgi network membrane 9/353 0.0000003 0.0000213 9 9.836361
39 GO:0002729 4 2.04e-04 31.67 2.00e-02 NA NA NA NA NA NA NA
207 GO:0030881 4 2.36e-04 30.15 2.00e-02 34 MF beta-2-microglobulin binding 4/353 0.0000304 0.0013995 4 20.268864
88 GO:0005886 107 3.71e-04 1.35 1.00e-02 246 CC plasma membrane 83/353 0.0936590 0.5933624 83 1.144574
78 GO:0005764 15 3.76e-04 3.11 1.00e-02 195 CC lysosome 8/353 0.0528559 0.4239312 8 1.964383
161 GO:0016020 62 3.87e-04 1.56 1.00e-02 56 CC membrane 56/353 0.0015514 0.0433270 56 1.489220
249 GO:0042608 4 6.69e-04 21.92 5.00e-02 NA NA NA NA NA NA NA
280 GO:0046977 3 8.08e-04 60.29 5.00e-02 NA NA NA NA NA NA NA
59 GO:0005436 4 8.81e-04 20.10 5.00e-02 NA NA NA NA NA NA NA
149 GO:0009986 22 1.11e-03 2.21 2.00e-02 43 CC cell surface 22/353 0.0003595 0.0130774 22 2.254166
162 GO:0016021 110 1.21e-03 1.30 2.00e-02 245 CC integral component of membrane 99/353 0.0934257 0.5933624 99 1.127313
1 GO:0000082 NA NA NA NA 736 BP G1/S transition of mitotic cell cycle 4/353 0.2870442 0.5933624 4 1.476540
2 GO:0000086 NA NA NA NA 631 BP G2/M transition of mitotic cell cycle 4/353 0.2474680 0.5933624 4 1.581259
3 GO:0000122 NA NA NA NA 1192 BP negative regulation of transcription from RNA polymerase II promoter 13/353 0.5182845 0.6800310 13 1.014863
4 GO:0000139 NA NA NA NA 62 CC Golgi membrane 20/353 0.0029982 0.0747582 20 1.983608
5 GO:0000151 NA NA NA NA 585 CC ubiquitin ligase complex 3/353 0.2287138 0.5933624 3 1.817588
6 GO:0000165 NA NA NA NA 806 BP MAPK cascade 6/353 0.3118678 0.5969064 6 1.306392

Compare p-values directly.

comparison_table$pvaluediff <- abs((comparison_table$PValue) - (comparison_table$pvalue))

hist( comparison_table$pvaluediff / (comparison_table$PValue) )

table( comparison_table$pvaluediff / (comparison_table$PValue) < 0.5)
## 
## FALSE  TRUE 
##    32     1
comparison_table$pvaluecheck  <-  comparison_table$pvaluediff / (comparison_table$PValue) < 0.5

Compare adjusted p-values directly.

comparison_table$fdrdiff <- abs(-log10(comparison_table$FDR) - -log10(comparison_table$p.adjust))

hist( comparison_table$fdrdiff / -log10(comparison_table$FDR) )

table(comparison_table$fdrdiff / -log10(comparison_table$FDR) < 1)
## 
## FALSE  TRUE 
##     1    32
comparison_table$fdrcheck  <- comparison_table$fdrdiff / -log10(comparison_table$FDR) < 1

Compare fold enrichments directly.

comparison_table$folddiff <- abs( comparison_table$Fold.Enrichment - comparison_table$EnrichmentScore)

hist( comparison_table$folddiff / comparison_table$Fold.Enrichment )

table( comparison_table$folddiff / comparison_table$Fold.Enrichment <0.3)
## 
## FALSE  TRUE 
##    14    19
comparison_table$foldcheck  <- comparison_table$folddiff / comparison_table$Fold.Enrichment <0.3

Now look at the significant sets and see if they classify as replicated.

sig <- subset(comparison_table, FDR <0.05)

#repro <- subset(sig, pvaluecheck == "TRUE")

repro <- subset(sig, fdrcheck == "TRUE" & foldcheck == "TRUE")

notrepro <- subset(sig, pvaluecheck != "TRUE")

message("No. significant results from paper")
## No. significant results from paper
nrow(sig)
## [1] 41
message("No. replicated results")
## No. replicated results
nrow(repro)
## [1] 19
message("No. non-replicated results")
## No. non-replicated results
nrow(notrepro)
## [1] 32
message("Success rate")
## Success rate
nrow(repro) / nrow(sig)
## [1] 0.4634146
head(repro,50) %>%
  kbl(caption="Top reproduced results") %>%
  kable_paper("hover", full_width = F)
Top reproduced results
GOID Count.x PValue Fold.Enrichment FDR S_No GO.Term GeneRatio pvalue p.adjust Count.y EnrichmentScore pvaluediff pvaluecheck fdrdiff fdrcheck folddiff foldcheck
38 GO:0002504 14 0.00e+00 44.34 0.00e+00 8 BP antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 10/353 0.0000000 0.0000000 10 37.159585 0.0000000 FALSE 3.6648395 TRUE 7.1804155 TRUE
251 GO:0042613 15 0.00e+00 36.91 0.00e+00 5 CC MHC class II protein complex 12/353 0.0000000 0.0000000 12 35.203817 0.0000000 FALSE 2.1236211 TRUE 1.7061831 TRUE
316 GO:0071556 15 0.00e+00 33.09 0.00e+00 2 CC integral component of lumenal side of endoplasmic reticulum membrane 15/353 0.0000000 0.0000000 15 29.860380 0.0000000 FALSE 0.5202894 TRUE 3.2296196 TRUE
220 GO:0032395 11 0.00e+00 51.02 0.00e+00 10 MF MHC class II receptor activity 8/353 0.0000000 0.0000000 8 40.537729 0.0000000 FALSE 3.4493557 TRUE 10.4822714 TRUE
248 GO:0042605 15 0.00e+00 24.44 0.00e+00 4 MF peptide antigen binding 15/353 0.0000000 0.0000000 15 23.888304 0.0000000 FALSE 1.2969421 TRUE 0.5516957 TRUE
157 GO:0012507 15 0.00e+00 17.14 0.00e+00 6 CC ER to Golgi transport vesicle membrane 15/353 0.0000000 0.0000000 15 17.063074 0.0000000 FALSE 1.0762871 TRUE 0.0769255 TRUE
115 GO:0006955 32 0.00e+00 4.12 0.00e+00 15 BP immune response 29/353 0.0000000 0.0000031 29 3.245867 0.0000000 FALSE 2.3222183 TRUE 0.8741327 TRUE
203 GO:0030658 11 0.00e+00 17.16 0.00e+00 11 CC transport vesicle membrane 11/353 0.0000000 0.0000000 11 17.031476 0.0000000 FALSE 1.1551666 TRUE 0.1285238 TRUE
250 GO:0042612 6 1.00e-07 42.65 5.80e-06 13 CC MHC class I protein complex 7/353 0.0000000 0.0000000 7 35.470512 0.0000001 FALSE 2.4372213 TRUE 7.1794875 TRUE
224 GO:0032729 11 4.00e-07 8.82 6.75e-05 36 BP positive regulation of interferon-gamma production 6/353 0.0001442 0.0062427 6 7.431917 0.0001438 FALSE 1.9660697 TRUE 1.3880831 TRUE
204 GO:0030666 10 1.50e-06 9.01 6.25e-05 19 CC endocytic vesicle membrane 10/353 0.0000003 0.0000213 10 8.445360 0.0000013 FALSE 0.4674855 TRUE 0.5646399 TRUE
32 GO:0002250 23 3.00e-06 3.23 4.25e-04 93 BP adaptive immune response 7/353 0.0128242 0.2074553 7 2.807019 0.0128212 FALSE 2.6885355 TRUE 0.4229810 TRUE
79 GO:0005765 19 2.48e-05 3.26 8.92e-04 32 CC lysosomal membrane 16/353 0.0000177 0.0008632 16 3.470156 0.0000071 TRUE 0.0142736 TRUE 0.2101558 TRUE
238 GO:0042102 8 7.11e-05 7.80 1.00e-02 31 BP positive regulation of T cell proliferation 8/353 0.0000087 0.0004387 8 7.688190 0.0000624 FALSE 1.3578099 TRUE 0.1118101 TRUE
206 GO:0030670 8 1.54e-04 6.92 4.53e-03 44 CC phagocytic vesicle membrane 6/353 0.0004417 0.0156994 6 6.080659 0.0002877 FALSE 0.5397836 TRUE 0.8393407 TRUE
88 GO:0005886 107 3.71e-04 1.35 1.00e-02 246 CC plasma membrane 83/353 0.0936590 0.5933624 83 1.144574 0.0932880 FALSE 1.7733200 TRUE 0.2054260 TRUE
161 GO:0016020 62 3.87e-04 1.56 1.00e-02 56 CC membrane 56/353 0.0015514 0.0433270 56 1.489220 0.0011644 FALSE 0.6367587 TRUE 0.0707800 TRUE
149 GO:0009986 22 1.11e-03 2.21 2.00e-02 43 CC cell surface 22/353 0.0003595 0.0130774 22 2.254166 0.0007505 FALSE 0.1845100 TRUE 0.0441660 TRUE
162 GO:0016021 110 1.21e-03 1.30 2.00e-02 245 CC integral component of membrane 99/353 0.0934257 0.5933624 99 1.127313 0.0922157 FALSE 1.4722900 TRUE 0.1726868 TRUE 
head(notrepro,50) %>%
  kbl(caption="Top un-reproduced results") %>%
  kable_paper("hover", full_width = F)
Top un-reproduced results
GOID Count.x PValue Fold.Enrichment FDR S_No GO.Term GeneRatio pvalue p.adjust Count.y EnrichmentScore pvaluediff pvaluecheck fdrdiff fdrcheck folddiff foldcheck
38 GO:0002504 14 0.00e+00 44.34 0.00e+00 8 BP antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 10/353 0.0000000 0.0000000 10 37.159585 0.0000000 FALSE 3.6648395 TRUE 7.1804155 TRUE
251 GO:0042613 15 0.00e+00 36.91 0.00e+00 5 CC MHC class II protein complex 12/353 0.0000000 0.0000000 12 35.203817 0.0000000 FALSE 2.1236211 TRUE 1.7061831 TRUE
316 GO:0071556 15 0.00e+00 33.09 0.00e+00 2 CC integral component of lumenal side of endoplasmic reticulum membrane 15/353 0.0000000 0.0000000 15 29.860380 0.0000000 FALSE 0.5202894 TRUE 3.2296196 TRUE
183 GO:0019882 17 0.00e+00 22.91 0.00e+00 29 BP antigen processing and presentation 7/353 0.0000044 0.0002377 7 10.267780 0.0000044 FALSE 10.4633105 TRUE 12.6422201 FALSE
220 GO:0032395 11 0.00e+00 51.02 0.00e+00 10 MF MHC class II receptor activity 8/353 0.0000000 0.0000000 8 40.537729 0.0000000 FALSE 3.4493557 TRUE 10.4822714 TRUE
248 GO:0042605 15 0.00e+00 24.44 0.00e+00 4 MF peptide antigen binding 15/353 0.0000000 0.0000000 15 23.888304 0.0000000 FALSE 1.2969421 TRUE 0.5516957 TRUE
292 GO:0050870 13 0.00e+00 24.95 0.00e+00 70 BP positive regulation of T cell activation 3/353 0.0038247 0.0854554 3 9.289896 0.0038247 FALSE 9.6788867 TRUE 15.6601039 FALSE
157 GO:0012507 15 0.00e+00 17.14 0.00e+00 6 CC ER to Golgi transport vesicle membrane 15/353 0.0000000 0.0000000 15 17.063074 0.0000000 FALSE 1.0762871 TRUE 0.0769255 TRUE
191 GO:0023026 12 0.00e+00 26.80 0.00e+00 30 MF MHC class II protein complex binding 5/353 0.0000067 0.0003497 5 17.418555 0.0000067 FALSE 6.9995706 TRUE 9.3814448 FALSE
184 GO:0019886 12 0.00e+00 25.34 0.00e+00 17 BP antigen processing and presentation of exogenous peptide antigen via MHC class II 12/353 0.0000001 0.0000085 12 7.270353 0.0000001 FALSE 4.7363662 TRUE 18.0696465 FALSE
115 GO:0006955 32 0.00e+00 4.12 0.00e+00 15 BP immune response 29/353 0.0000000 0.0000031 29 3.245867 0.0000000 FALSE 2.3222183 TRUE 0.8741327 TRUE
203 GO:0030658 11 0.00e+00 17.16 0.00e+00 11 CC transport vesicle membrane 11/353 0.0000000 0.0000000 11 17.031476 0.0000000 FALSE 1.1551666 TRUE 0.1285238 TRUE
291 GO:0050852 15 0.00e+00 8.48 6.00e-07 22 BP T cell receptor signaling pathway 14/353 0.0000009 0.0000609 14 5.002252 0.0000009 FALSE 2.0198128 TRUE 3.4777482 FALSE
148 GO:0009897 27 0.00e+00 3.79 9.00e-07 807 CC external side of plasma membrane 5/353 0.3146044 0.5969064 5 1.346362 0.3146044 FALSE 5.8004745 TRUE 2.4436382 FALSE
250 GO:0042612 6 1.00e-07 42.65 5.80e-06 13 CC MHC class I protein complex 7/353 0.0000000 0.0000000 7 35.470512 0.0000001 FALSE 2.4372213 TRUE 7.1794875 TRUE
26 GO:0001916 8 2.00e-07 18.77 2.51e-05 54 BP positive regulation of T cell mediated cytotoxicity 3/353 0.0014326 0.0407391 3 12.862933 0.0014325 FALSE 3.2103375 TRUE 5.9070669 FALSE
55 GO:0005102 24 2.00e-07 3.65 2.47e-05 49 MF receptor binding 16/353 0.0008973 0.0286393 16 2.463619 0.0008971 FALSE 3.0642661 TRUE 1.1863811 FALSE
224 GO:0032729 11 4.00e-07 8.82 6.75e-05 36 BP positive regulation of interferon-gamma production 6/353 0.0001442 0.0062427 6 7.431917 0.0001438 FALSE 1.9660697 TRUE 1.3880831 TRUE
205 GO:0030669 10 1.40e-06 9.14 6.25e-05 16 CC clathrin-coated endocytic vesicle membrane 9/353 0.0000000 0.0000036 9 12.235473 0.0000013 FALSE 1.2406865 TRUE 3.0954729 FALSE
204 GO:0030666 10 1.50e-06 9.01 6.25e-05 19 CC endocytic vesicle membrane 10/353 0.0000003 0.0000213 10 8.445360 0.0000013 FALSE 0.4674855 TRUE 0.5646399 TRUE
32 GO:0002250 23 3.00e-06 3.23 4.25e-04 93 BP adaptive immune response 7/353 0.0128242 0.2074553 7 2.807019 0.0128212 FALSE 2.6885355 TRUE 0.4229810 TRUE
150 GO:0010008 15 4.65e-05 3.79 1.51e-03 110 CC endosome membrane 8/353 0.0177282 0.2490753 8 2.436694 0.0176817 FALSE 2.2173537 TRUE 1.3533059 FALSE
238 GO:0042102 8 7.11e-05 7.80 1.00e-02 31 BP positive regulation of T cell proliferation 8/353 0.0000087 0.0004387 8 7.688190 0.0000624 FALSE 1.3578099 TRUE 0.1118101 TRUE
25 GO:0001819 8 7.84e-05 7.68 1.00e-02 27 BP positive regulation of cytokine production 6/353 0.0000033 0.0001896 6 13.934844 0.0000751 FALSE 1.7221086 TRUE 6.2548442 FALSE
206 GO:0030670 8 1.54e-04 6.92 4.53e-03 44 CC phagocytic vesicle membrane 6/353 0.0004417 0.0156994 6 6.080659 0.0002877 FALSE 0.5397836 TRUE 0.8393407 TRUE
223 GO:0032588 9 1.96e-04 5.64 1.00e-02 20 CC trans-Golgi network membrane 9/353 0.0000003 0.0000213 9 9.836361 0.0001957 FALSE 2.6716055 FALSE 4.1963606 FALSE
207 GO:0030881 4 2.36e-04 30.15 2.00e-02 34 MF beta-2-microglobulin binding 4/353 0.0000304 0.0013995 4 20.268864 0.0002056 FALSE 1.1550628 TRUE 9.8811357 FALSE
88 GO:0005886 107 3.71e-04 1.35 1.00e-02 246 CC plasma membrane 83/353 0.0936590 0.5933624 83 1.144574 0.0932880 FALSE 1.7733200 TRUE 0.2054260 TRUE
78 GO:0005764 15 3.76e-04 3.11 1.00e-02 195 CC lysosome 8/353 0.0528559 0.4239312 8 1.964383 0.0524799 FALSE 1.6272954 TRUE 1.1456167 FALSE
161 GO:0016020 62 3.87e-04 1.56 1.00e-02 56 CC membrane 56/353 0.0015514 0.0433270 56 1.489220 0.0011644 FALSE 0.6367587 TRUE 0.0707800 TRUE
149 GO:0009986 22 1.11e-03 2.21 2.00e-02 43 CC cell surface 22/353 0.0003595 0.0130774 22 2.254166 0.0007505 FALSE 0.1845100 TRUE 0.0441660 TRUE
162 GO:0016021 110 1.21e-03 1.30 2.00e-02 245 CC integral component of membrane 99/353 0.0934257 0.5933624 99 1.127313 0.0922157 FALSE 1.4722900 TRUE 0.1726868 TRUE

Session information

For reproducibility

sessionInfo()
## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
##  [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
##  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] eulerr_7.0.2     lubridate_1.9.3  forcats_1.0.0    stringr_1.5.1   
##  [5] dplyr_1.1.4      purrr_1.0.2      readr_2.1.5      tidyr_1.3.1     
##  [9] tibble_3.2.1     ggplot2_3.5.1    tidyverse_2.0.0  kableExtra_1.4.0
## [13] knitr_1.47      
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    xml2_1.3.6       
##  [5] polylabelr_0.2.0  stringi_1.8.4     hms_1.1.3         digest_0.6.35    
##  [9] magrittr_2.0.3    evaluate_0.24.0   grid_4.4.0        timechange_0.3.0 
## [13] fastmap_1.2.0     jsonlite_1.8.8    fansi_1.0.6       viridisLite_0.4.2
## [17] scales_1.3.0      jquerylib_0.1.4   cli_3.6.2         rlang_1.1.4      
## [21] polyclip_1.10-6   munsell_0.5.1     withr_3.0.0       cachem_1.1.0     
## [25] yaml_2.3.8        tools_4.4.0       tzdb_0.4.0        colorspace_2.1-0 
## [29] vctrs_0.6.5       R6_2.5.1          lifecycle_1.0.4   pkgconfig_2.0.3  
## [33] pillar_1.9.0      bslib_0.7.0       gtable_0.3.5      glue_1.7.0       
## [37] Rcpp_1.0.12       systemfonts_1.1.0 xfun_0.44         tidyselect_1.2.1 
## [41] highr_0.11        rstudioapi_0.16.0 htmltools_0.5.8.1 rmarkdown_2.27   
## [45] svglite_2.1.3     compiler_4.4.0