424 unique samples | DLPFC region | ROSMAP cohort

Cell types

Excitatory Neurons

## [1] "Cytokines expressed in excitatory neurons and used in GSEA:"
##  [1] "TNFSF4"   "THPO"     "CXCL13"   "SPP1"     "EGF"      "FGF2"    
##  [7] "IL15"     "CCL28"    "CXCL14"   "VEGFA"    "HGF"      "IL7"     
## [13] "C5"       "IL18"     "KITLG"    "IL17D"    "TNFSF13B" "IL16"    
## [19] "CX3CL1"   "IL34"     "TNFSF12"  "PSPN"     "TNFSF9"   "TGFB1"   
## [25] "CXCL17"
gostres_ext <- gost(query = list_expr_ext, significant = TRUE, organism = "hsapiens")
createDT(gostres_ext$result %>% arrange(p_value))
gostplot(gostres_ext, interactive = TRUE)

Inhibitory Neurons

## [1] "Cytokines expressed in inhbitory neurons and used in GSEA:"
##  [1] "TNFSF4"   "CXCL13"   "SPP1"     "EGF"      "FGF2"     "IL15"    
##  [7] "CXCL14"   "VEGFA"    "HGF"      "IL7"      "C5"       "IL18"    
## [13] "KITLG"    "DCN"      "IGF1"     "IL17D"    "TNFSF13B" "IL16"    
## [19] "CX3CL1"   "IL34"     "TNFSF12"  "NOG"      "PSPN"     "TNFSF9"  
## [25] "C3"       "TGFB1"
gostres_inh <- gost(query = list_expr_inh, significant = TRUE, organism = "hsapiens")
createDT(gostres_inh$result %>% arrange(p_value))
gostplot(gostres_inh, interactive = TRUE)

Microglia

## [1] "Cytokines expressed in microglia and used in GSEA:"
##  [1] "IL1A"     "IL1B"     "TNFSF10"  "SPP1"     "FGF2"     "IL15"    
##  [7] "CXCL14"   "VEGFA"    "HGF"      "IL7"      "TNFSF8"   "C5"      
## [13] "IL18"     "KITLG"    "IGF1"     "IL17D"    "TNFSF13B" "IL16"    
## [19] "CX3CL1"   "IL34"     "TNFSF12"  "TNFSF13"  "EBI3"     "C3"      
## [25] "TGFB1"    "FLT3LG"
gostres_mic <- gost(query = list_expr_mic, significant = TRUE, organism = "hsapiens")
createDT(gostres_mic$result %>% arrange(p_value))
gostplot(gostres_mic, interactive = TRUE)

Astrocytes

## [1] "Cytokines expressed in astrocytes and used in GSEA:"
##  [1] "CSF1"     "TNFSF4"   "SPP1"     "EGF"      "FGF2"     "IL15"    
##  [7] "CXCL14"   "VEGFA"    "HGF"      "IL7"      "IL33"     "C5"      
## [13] "IL18"     "KITLG"    "DCN"      "IL17D"    "TNFSF13B" "CTF1"    
## [19] "CX3CL1"   "IL34"     "TNFSF12"  "TNFSF13"  "PSPN"     "C3"      
## [25] "TGFB1"    "CXCL17"   "FLT3LG"
gostres_ast <- gost(query = list_expr_ast, significant = TRUE, organism = "hsapiens")
createDT(gostres_ast$result %>% arrange(p_value))
gostplot(gostres_ast, interactive = TRUE)

Oligodendrocytes

## [1] "Cytokines expressed in oligodendrocytes and used in GSEA:"
##  [1] "CSF1"     "TNFSF4"   "SPP1"     "FGF2"     "GDNF"     "CXCL14"  
##  [7] "VEGFA"    "HGF"      "IL7"      "IFNA13"   "IFNA2"    "C5"      
## [13] "IL18"     "KITLG"    "DCN"      "IGF1"     "IL17D"    "TNFSF13B"
## [19] "CX3CL1"   "IL34"     "TNFSF12"  "TNFSF13"  "PSPN"     "TNFSF9"  
## [25] "C3"       "TGFB1"    "CXCL17"
gostres_oli <- gost(query = list_expr_oli, significant = TRUE, organism = "hsapiens")
createDT(gostres_oli$result %>% arrange(p_value))
gostplot(gostres_oli, interactive = TRUE)

OPC cells

## [1] "Cytokines expressed in eOPC cells and used in GSEA:"
##  [1] "CSF1"     "SPP1"     "FGF2"     "GDNF"     "CXCL14"   "VEGFA"   
##  [7] "IL7"      "C5"       "IL18"     "KITLG"    "IL17D"    "TNFSF13B"
## [13] "CX3CL1"   "IL34"     "TNFSF12"  "TNFSF13"  "TGFB1"    "CXCL17"  
## [19] "FLT3LG"
gostres_opc <- gost(query = list_expr_opc, significant = TRUE, organism = "hsapiens")
createDT(gostres_opc$result %>% arrange(p_value))
gostplot(gostres_opc, interactive = TRUE)

Endothelial cells

## [1] "Cytokines expressed in endothelial cells and used in GSEA:"
##  [1] "TNFSF10" "SPP1"    "FGF2"    "IL15"    "KITLG"   "DCN"     "IL32"   
##  [8] "CX3CL1"  "TNFSF12" "TGFB1"
gostres_end <- gost(query = list_expr_end, significant = TRUE, organism = "hsapiens")
createDT(gostres_end$result %>% arrange(p_value))
gostplot(gostres_end, 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