Overlap of GO Terms in DEGs
Last updated: 2025-02-20
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 2e99243 | sayanpaul01 | 2025-02-20 | Build site. |
| Rmd | 7f9dc02 | sayanpaul01 | 2025-02-20 | Added Overlap of GO Terms in DEGs and updated index |
📌 Load Required Libraries
library(ggVennDiagram)
library(ggplot2)
library(dplyr)📌 Read and Process GO Terms
# Load GO term data for different conditions
# Load GO term data for different conditions
CX_0.1_24_GO <- read.csv("data/CX_0.1_24 (Combined).csv")
CX_0.1_48_GO <- read.csv("data/CX_0.1_48 (Combined).csv")
CX_0.5_3_GO <- read.csv("data/CX_0.5_3 (Combined).csv")
CX_0.5_24_GO <- read.csv("data/CX_0.5_24 (Combined).csv")
CX_0.5_48_GO <- read.csv("data/CX_0.5_48 (Combined).csv")
DOX_0.1_3_GO <- read.csv("data/DOX_0.1_3 (Combined).csv")
DOX_0.1_24_GO <- read.csv("data/DOX_0.1_24 (Combined).csv")
DOX_0.1_48_GO <- read.csv("data/DOX_0.1_48 (Combined).csv")
DOX_0.5_3_GO <- read.csv("data/DOX_0.5_3 (Combined).csv")
DOX_0.5_24_GO <- read.csv("data/DOX_0.5_24 (Combined).csv")
DOX_0.5_48_GO <- read.csv("data/DOX_0.5_48 (Combined).csv")
# Extract GO term IDs for each condition
DEG2_GO <- CX_0.1_24_GO$ID
DEG3_GO <- CX_0.1_48_GO$ID
DEG4_GO <- CX_0.5_3_GO$ID
DEG5_GO <- CX_0.5_24_GO$ID
DEG6_GO <- CX_0.5_48_GO$ID
DEG7_GO <- DOX_0.1_3_GO$ID
DEG8_GO <- DOX_0.1_24_GO$ID
DEG9_GO <- DOX_0.1_48_GO$ID
DEG10_GO <- DOX_0.5_3_GO$ID
DEG11_GO <- DOX_0.5_24_GO$ID
DEG12_GO <- DOX_0.5_48_GO$term_id📌 Overlap of GO Terms across the drugs
📌 Overlap of GO Terms in CX-5461 vs VEH
CX_Datasets <- list(
"CX_0.1_24" = DEG2_GO,
"CX_0.1_48" = DEG3_GO,
"CX_0.5_3" = DEG4_GO,
"CX_0.5_24" = DEG5_GO,
"CX_0.5_48" = DEG6_GO
)
ggVennDiagram(CX_Datasets, label = "count") +
theme(
plot.title = element_text(size = 16, face = "bold"),
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10)
) +
labs(title = "CX-5461 GO Term Overlap")
| Version | Author | Date |
|---|---|---|
| 2e99243 | sayanpaul01 | 2025-02-20 |
📌 Overlap of GO Terms in DOX vs VEH
DOX_Datasets <- list(
"DOX_0.1_3" = DEG7_GO,
"DOX_0.1_24" = DEG8_GO,
"DOX_0.1_48" = DEG9_GO,
"DOX_0.5_3" = DEG10_GO,
"DOX_0.5_24" = DEG11_GO,
"DOX_0.5_48" = DEG12_GO
)
ggVennDiagram(DOX_Datasets, label = "count") +
theme(
plot.title = element_text(size = 16, face = "bold"),
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10)
) +
labs(title = "DOX GO Term Overlap")
| Version | Author | Date |
|---|---|---|
| 2e99243 | sayanpaul01 | 2025-02-20 |
📌 Overlap of GO Terms across concentrations
📌 0.1 µM Concentration
Concentration_0_1 <- list(
"CX_0.1_24" = DEG2_GO,
"CX_0.1_48" = DEG3_GO,
"DOX_0.1_3" = DEG7_GO,
"DOX_0.1_24" = DEG8_GO,
"DOX_0.1_48" = DEG9_GO
)
ggVennDiagram(Concentration_0_1, label = "count") +
theme(
plot.title = element_text(size = 16, face = "bold"),
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10)
) +
labs(title = "0.1 µM GO Term Overlap")
| Version | Author | Date |
|---|---|---|
| 2e99243 | sayanpaul01 | 2025-02-20 |
📌 0.5 µM Concentration
Concentration_0_5 <- list(
"CX_0.5_3" = DEG4_GO,
"CX_0.5_24" = DEG5_GO,
"CX_0.5_48" = DEG6_GO,
"DOX_0.5_3" = DEG10_GO,
"DOX_0.5_24" = DEG11_GO,
"DOX_0.5_48" = DEG12_GO
)
ggVennDiagram(Concentration_0_5, label = "count") +
theme(
plot.title = element_text(size = 16, face = "bold"),
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10)
) +
labs(title = "0.5 µM GO Term Overlap")
| Version | Author | Date |
|---|---|---|
| 2e99243 | sayanpaul01 | 2025-02-20 |
📌 Overlap of GO Terms Across Timepoints
📌3 Hours
Timepoint_3hrs <- list(
"CX_0.5_3" = DEG4_GO,
"DOX_0.1_3" = DEG7_GO,
"DOX_0.5_3" = DEG10_GO
)
ggVennDiagram(Timepoint_3hrs, label = "count") +
theme(
plot.title = element_text(size = 16, face = "bold"),
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10)
) +
labs(title = "3 Hours GO Term Overlap")
| Version | Author | Date |
|---|---|---|
| 2e99243 | sayanpaul01 | 2025-02-20 |
📌24 Hours
Timepoint_24hrs <- list(
"CX_0.1_24" = DEG2_GO,
"CX_0.5_24" = DEG5_GO,
"DOX_0.1_24" = DEG8_GO,
"DOX_0.5_24" = DEG11_GO
)
ggVennDiagram(Timepoint_24hrs, label = "count") +
theme(
plot.title = element_text(size = 16, face = "bold"),
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10)
) +
labs(title = "24 Hours GO Term Overlap")
| Version | Author | Date |
|---|---|---|
| 2e99243 | sayanpaul01 | 2025-02-20 |
📌48 Hours
Timepoint_48hrs <- list(
"CX_0.1_48" = DEG3_GO,
"CX_0.5_48" = DEG6_GO,
"DOX_0.1_48" = DEG9_GO,
"DOX_0.5_48" = DEG12_GO
)
ggVennDiagram(Timepoint_48hrs, label = "count") +
theme(
plot.title = element_text(size = 16, face = "bold"),
legend.title = element_text(size = 12, face = "bold"),
legend.text = element_text(size = 10)
) +
labs(title = "48 Hours GO Term Overlap")
| Version | Author | Date |
|---|---|---|
| 2e99243 | sayanpaul01 | 2025-02-20 |
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.1.4 ggplot2_3.5.1 ggVennDiagram_1.5.2
[4] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 jsonlite_1.8.9 compiler_4.3.0 promises_1.3.0
[5] tidyselect_1.2.1 Rcpp_1.0.12 stringr_1.5.1 git2r_0.35.0
[9] callr_3.7.6 later_1.3.2 jquerylib_0.1.4 scales_1.3.0
[13] yaml_2.3.10 fastmap_1.1.1 R6_2.5.1 labeling_0.4.3
[17] generics_0.1.3 knitr_1.49 tibble_3.2.1 munsell_0.5.1
[21] rprojroot_2.0.4 bslib_0.8.0 pillar_1.10.1 rlang_1.1.3
[25] cachem_1.0.8 stringi_1.8.3 httpuv_1.6.15 xfun_0.50
[29] getPass_0.2-4 fs_1.6.3 sass_0.4.9 cli_3.6.1
[33] withr_3.0.2 magrittr_2.0.3 ps_1.8.1 digest_0.6.34
[37] grid_4.3.0 processx_3.8.5 rstudioapi_0.17.1 lifecycle_1.0.4
[41] vctrs_0.6.5 evaluate_1.0.3 glue_1.7.0 farver_2.1.2
[45] whisker_0.4.1 colorspace_2.1-0 rmarkdown_2.29 httr_1.4.7
[49] tools_4.3.0 pkgconfig_2.0.3 htmltools_0.5.8.1