424 unique samples | DLPFC region | ROSMAP cohort

GSEA

## [1] "Cytokines expressed in bulk ROSMAP data and used in GSEA:"
##  [1] "CX3CL1"   "IL32"     "DCN"      "IGF1"     "HGF"      "KITLG"   
##  [7] "CXCL2"    "THPO"     "FLT3LG"   "IL11"     "TNFSF13B" "EBI3"    
## [13] "TGFB1"    "C5"       "CCL2"     "VEGFA"    "TNFSF4"   "SPP1"    
## [19] "TNFSF10"  "IL1B"     "PSPN"     "TNFSF9"   "C3"       "IL33"    
## [25] "FGF2"     "EGF"      "CXCL14"   "CTF1"     "IL18"     "CCL28"   
## [31] "IL34"     "TNFSF13"  "CXCL5"    "IL15"     "GDNF"     "IL12A"   
## [37] "CXCL8"    "IL16"     "IL17D"    "NOG"      "CSF1"     "TNFSF12"
gostres <- gost(query = list_expr_bulk, significant = TRUE, organism = "hsapiens")
createDT(gostres$result %>% arrange(p_value))
gostplot(gostres, interactive = TRUE)

Session info

sessionInfo()
## R version 4.3.2 (2023-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 11 x64 (build 26100)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=Portuguese_Brazil.utf8  LC_CTYPE=Portuguese_Brazil.utf8   
## [3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C                      
## [5] LC_TIME=Portuguese_Brazil.utf8    
## 
## time zone: America/Sao_Paulo
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] dplyr_1.1.4      gprofiler2_0.2.3
## 
## loaded via a namespace (and not attached):
##  [1] plotly_4.10.4     sass_0.4.9        utf8_1.2.4        generics_0.1.3   
##  [5] tidyr_1.3.1       bitops_1.0-8      digest_0.6.36     magrittr_2.0.3   
##  [9] evaluate_0.24.0   grid_4.3.2        fastmap_1.2.0     jsonlite_1.8.8   
## [13] promises_1.3.0    httr_1.4.7        purrr_1.0.2       fansi_1.0.6      
## [17] crosstalk_1.2.1   viridisLite_0.4.2 scales_1.3.0      lazyeval_0.2.2   
## [21] jquerylib_0.1.4   cli_3.6.2         shiny_1.9.1       rlang_1.1.3      
## [25] munsell_0.5.1     withr_3.0.1       cachem_1.1.0      yaml_2.3.10      
## [29] tools_4.3.2       colorspace_2.1-0  ggplot2_3.5.0     httpuv_1.6.15    
## [33] DT_0.33           vctrs_0.6.5       R6_2.5.1          mime_0.12        
## [37] lifecycle_1.0.4   htmlwidgets_1.6.4 pkgconfig_2.0.3   pillar_1.9.0     
## [41] bslib_0.8.0       later_1.3.2       gtable_0.3.5      data.table_1.15.4
## [45] glue_1.7.0        Rcpp_1.0.12       xfun_0.46         tibble_3.2.1     
## [49] tidyselect_1.2.1  rstudioapi_0.16.0 knitr_1.48        xtable_1.8-4     
## [53] htmltools_0.5.8.1 rmarkdown_2.27    compiler_4.3.2    RCurl_1.98-1.16