KEGG enrichment of differential protein expression results

## 

## clusterProfiler v4.16.0 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
## 
## Please cite:
## 
## S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
## W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
## multiomics data. Nature Protocols. 2024, 19(11):3292-3320

## 
## Attaching package: 'clusterProfiler'

## The following object is masked from 'package:stats':
## 
##     filter

## Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...

## Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...

## Reading KEGG annotation online: "https://rest.kegg.jp/conv/uniprot/hsa"...

## using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

## preparing geneSet collections...

## GSEA analysis...

## leading edge analysis...

## done...

## R version 4.5.1 (2025-06-13 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows 11 x64 (build 26100)
## 
## Matrix products: default
##   LAPACK version 3.12.1
## 
## 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/Los_Angeles
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices datasets  utils     methods   base     
## 
## other attached packages:
## [1] kableExtra_1.4.0       clusterProfiler_4.16.0
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3               gson_0.1.0              rlang_1.1.6            
##   [4] magrittr_2.0.3          DOSE_4.2.0              compiler_4.5.1         
##   [7] RSQLite_2.4.3           systemfonts_1.2.3       png_0.1-8              
##  [10] vctrs_0.6.5             reshape2_1.4.4          stringr_1.5.1          
##  [13] pkgconfig_2.0.3         crayon_1.5.3            fastmap_1.2.0          
##  [16] XVector_0.48.0          labeling_0.4.3          rmarkdown_2.29         
##  [19] enrichplot_1.28.4       UCSC.utils_1.4.0        purrr_1.1.0            
##  [22] bit_4.6.0               xfun_0.53               cachem_1.1.0           
##  [25] aplot_0.2.8             GenomeInfoDb_1.44.2     jsonlite_2.0.0         
##  [28] blob_1.2.4              BiocParallel_1.42.1     parallel_4.5.1         
##  [31] R6_2.6.1                bslib_0.9.0             stringi_1.8.7          
##  [34] RColorBrewer_1.1-3      jquerylib_0.1.4         GOSemSim_2.34.0        
##  [37] Rcpp_1.1.0              knitr_1.50              snow_0.4-4             
##  [40] ggtangle_0.0.7          R.utils_2.13.0          IRanges_2.42.0         
##  [43] Matrix_1.7-3            splines_4.5.1           igraph_2.1.4           
##  [46] tidyselect_1.2.1        qvalue_2.40.0           rstudioapi_0.17.1      
##  [49] yaml_2.3.10             codetools_0.2-20        lattice_0.22-7         
##  [52] tibble_3.3.0            plyr_1.8.9              withr_3.0.2            
##  [55] Biobase_2.68.0          treeio_1.32.0           KEGGREST_1.48.1        
##  [58] evaluate_1.0.4          gridGraphics_0.5-1      xml2_1.4.0             
##  [61] Biostrings_2.76.0       pillar_1.11.0           BiocManager_1.30.26    
##  [64] ggtree_3.16.3           renv_1.1.5              stats4_4.5.1           
##  [67] ggfun_0.2.0             generics_0.1.4          S4Vectors_0.46.0       
##  [70] ggplot2_3.5.2           scales_1.4.0            tidytree_0.4.6         
##  [73] glue_1.8.0              lazyeval_0.2.2          tools_4.5.1            
##  [76] ggnewscale_0.5.2        data.table_1.17.8       fgsea_1.34.2           
##  [79] fs_1.6.6                fastmatch_1.1-6         cowplot_1.2.0          
##  [82] grid_4.5.1              tidyr_1.3.1             ape_5.8-1              
##  [85] AnnotationDbi_1.70.0    colorspace_2.1-1        nlme_3.1-168           
##  [88] GenomeInfoDbData_1.2.14 patchwork_1.3.2         cli_3.6.5              
##  [91] rappdirs_0.3.3          textshaping_1.0.1       viridisLite_0.4.2      
##  [94] svglite_2.2.1           dplyr_1.1.4             gtable_0.3.6           
##  [97] R.methodsS3_1.8.2       yulab.utils_0.2.1       sass_0.4.10            
## [100] digest_0.6.37           BiocGenerics_0.54.0     ggrepel_0.9.6          
## [103] ggplotify_0.1.2         farver_2.1.2            memoise_2.0.1          
## [106] htmltools_0.5.8.1       R.oo_1.27.1             lifecycle_1.0.4        
## [109] httr_1.4.7              GO.db_3.21.0            bit64_4.6.0-1