Last updated: 2023-02-01
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Knit directory: Cardiotoxicity/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 1657edd | reneeisnowhere | 2023-02-01 | updating Go tables |
| html | eed4dc5 | reneeisnowhere | 2023-01-31 | Build site. |
| Rmd | 848eb1a | reneeisnowhere | 2023-01-31 | updating GO plots |
| Rmd | 82b31a0 | reneeisnowhere | 2023-01-31 | updating GEA |
| Rmd | 34a525c | reneeisnowhere | 2023-01-26 | link update |
| html | 41b5f9c | reneeisnowhere | 2023-01-23 | Build site. |
| Rmd | dc890ec | reneeisnowhere | 2023-01-23 | Updating the source dir |
| Rmd | a78eab0 | reneeisnowhere | 2023-01-23 | updated Go analysis |
| Rmd | d9edc06 | reneeisnowhere | 2023-01-20 | try a little update later |
| Rmd | b7eac76 | reneeisnowhere | 2023-01-20 | updating GO |
| html | 6c21cf8 | reneeisnowhere | 2023-01-20 | Build site. |
| Rmd | 443a9f3 | reneeisnowhere | 2023-01-20 | adding in GO analysis |
I have created several files from the RNA analysis that contain the significant genes(determined by adj.P.val < 0.1) from each Time and Condition. The names of the files are in the following format: ‘sigV’+Drug(2 letters)+time.
example: ‘sigVDA3.txt’ means this file contains the significant DE genes from the Daunorubicin 3 hour compared to Vehicle Control 3 hour analysis
library(gprofiler2)
library(tidyverse)
library(readr)
library(BiocGenerics)
library(gridExtra)
library(VennDiagram)
library(kableExtra)
library(scales)The analysis is based on all genes that passed the rowMeans>0 from the previous page link
Below is the analysis of differentially expressed genes for each treatment at 3 hours and 24 hours.
| source | term_id | term_name | intersection_size | term_size | p_value |
|---|---|---|---|---|---|
| GO:BP | GO:0006366 | transcription by RNA polymerase II | 212 | 2055 | 1.51e-31 |
| GO:BP | GO:0006357 | regulation of transcription by RNA polymerase II | 206 | 1978 | 3.06e-31 |
| GO:BP | GO:0097659 | nucleic acid-templated transcription | 243 | 2767 | 3.81e-27 |
| GO:BP | GO:0006351 | DNA-templated transcription | 243 | 2766 | 3.81e-27 |
| GO:BP | GO:0032774 | RNA biosynthetic process | 243 | 2782 | 7.23e-27 |
| GO:BP | GO:0051252 | regulation of RNA metabolic process | 247 | 2921 | 1.06e-25 |
| GO:BP | GO:1903506 | regulation of nucleic acid-templated transcription | 234 | 2663 | 1.13e-25 |
| GO:BP | GO:0006355 | regulation of DNA-templated transcription | 234 | 2662 | 1.13e-25 |
| GO:BP | GO:2001141 | regulation of RNA biosynthetic process | 234 | 2670 | 1.50e-25 |
| GO:BP | GO:0010556 | regulation of macromolecule biosynthetic process | 248 | 3088 | 3.55e-23 |
| GO:BP | GO:0019219 | regulation of nucleobase-containing compound metabolic process | 214 | 3181 | 7.80e-23 |
| GO:BP | GO:0034654 | nucleobase-containing compound biosynthetic process | 202 | 3149 | 3.21e-21 |
| GO:BP | GO:0031326 | regulation of cellular biosynthetic process | 211 | 3204 | 3.83e-21 |
| GO:BP | GO:0018130 | heterocycle biosynthetic process | 249 | 3210 | 7.32e-21 |
| GO:BP | GO:0019438 | aromatic compound biosynthetic process | 186 | 3212 | 1.37e-20 |
| GO:BP | GO:0009889 | regulation of biosynthetic process | 211 | 3255 | 2.37e-20 |
| GO:BP | GO:1901362 | organic cyclic compound biosynthetic process | 188 | 3319 | 1.13e-19 |
| GO:BP | GO:0009059 | macromolecule biosynthetic process | 220 | 3801 | 3.12e-19 |
| GO:BP | GO:0044271 | cellular nitrogen compound biosynthetic process | 222 | 3820 | 3.95e-16 |
| GO:BP | GO:0031323 | regulation of cellular metabolic process | 234 | 4432 | 1.89e-15 |
| GO:BP | GO:0080090 | regulation of primary metabolic process | 234 | 4567 | 3.53e-13 |
| GO:BP | GO:0051171 | regulation of nitrogen compound metabolic process | 239 | 4443 | 4.83e-13 |
| GO:BP | GO:0044249 | cellular biosynthetic process | 208 | 4569 | 2.48e-12 |
| GO:BP | GO:0000122 | negative regulation of transcription by RNA polymerase II | 83 | 761 | 2.91e-12 |
| GO:BP | GO:1901576 | organic substance biosynthetic process | 208 | 4628 | 1.02e-11 |
| GO:BP | GO:0045892 | negative regulation of DNA-templated transcription | 100 | 1041 | 1.05e-11 |
| GO:BP | GO:1903507 | negative regulation of nucleic acid-templated transcription | 100 | 1043 | 1.12e-11 |
| GO:BP | GO:1902679 | negative regulation of RNA biosynthetic process | 100 | 1044 | 1.19e-11 |
| GO:BP | GO:0051253 | negative regulation of RNA metabolic process | 105 | 1137 | 1.71e-11 |
| GO:BP | GO:0009058 | biosynthetic process | 209 | 4691 | 2.15e-11 |
| GO:BP | GO:0010558 | negative regulation of macromolecule biosynthetic process | 106 | 1237 | 1.20e-09 |
| GO:BP | GO:0045934 | negative regulation of nucleobase-containing compound metabolic process | 106 | 1239 | 1.41e-09 |
| GO:BP | GO:0045893 | positive regulation of DNA-templated transcription | 108 | 1342 | 3.35e-09 |
| GO:BP | GO:1903508 | positive regulation of nucleic acid-templated transcription | 108 | 1342 | 3.35e-09 |
| GO:BP | GO:0010468 | regulation of gene expression | 212 | 3687 | 3.35e-09 |
| GO:BP | GO:0051254 | positive regulation of RNA metabolic process | 114 | 1469 | 3.59e-09 |
| GO:BP | GO:1902680 | positive regulation of RNA biosynthetic process | 108 | 1348 | 3.93e-09 |
| GO:BP | GO:0031327 | negative regulation of cellular biosynthetic process | 106 | 1279 | 9.70e-09 |
| GO:BP | GO:0010557 | positive regulation of macromolecule biosynthetic process | 116 | 1537 | 1.15e-08 |
| GO:BP | GO:0009890 | negative regulation of biosynthetic process | 106 | 1304 | 2.77e-08 |
| GO:BP | GO:0031328 | positive regulation of cellular biosynthetic process | 119 | 1614 | 3.64e-08 |
| GO:BP | GO:0045944 | positive regulation of transcription by RNA polymerase II | 83 | 952 | 8.69e-08 |
| GO:BP | GO:0009891 | positive regulation of biosynthetic process | 119 | 1640 | 1.04e-07 |
| GO:BP | GO:0045935 | positive regulation of nucleobase-containing compound metabolic process | 117 | 1641 | 2.23e-07 |
| GO:BP | GO:0031324 | negative regulation of cellular metabolic process | 127 | 1830 | 8.08e-07 |
| GO:BP | GO:0060255 | regulation of macromolecule metabolic process | 111 | 4772 | 2.49e-06 |
| GO:BP | GO:0019222 | regulation of metabolic process | 115 | 5189 | 1.10e-05 |
| GO:BP | GO:0031325 | positive regulation of cellular metabolic process | 123 | 2446 | 1.78e-05 |
| GO:BP | GO:0051173 | positive regulation of nitrogen compound metabolic process | 123 | 2497 | 5.00e-05 |
| GO:BP | GO:0051172 | negative regulation of nitrogen compound metabolic process | 126 | 1905 | 5.02e-05 |
| GO:CC | GO:0090575 | RNA polymerase II transcription regulator complex | 14 | 219 | 3.93e-05 |
| GO:CC | GO:0005667 | transcription regulator complex | 42 | 413 | 3.93e-05 |
| GO:MF | GO:0003677 | DNA binding | 197 | 1908 | 9.77e-29 |
| GO:MF | GO:0140110 | transcription regulator activity | 168 | 1431 | 1.30e-28 |
| GO:MF | GO:0000976 | transcription cis-regulatory region binding | 143 | 1082 | 4.97e-28 |
| GO:MF | GO:0001067 | transcription regulatory region nucleic acid binding | 143 | 1084 | 4.97e-28 |
| GO:MF | GO:0003700 | DNA-binding transcription factor activity | 138 | 975 | 4.97e-28 |
| GO:MF | GO:0000977 | RNA polymerase II transcription regulatory region sequence-specific DNA binding | 136 | 998 | 3.16e-27 |
| GO:MF | GO:1990837 | sequence-specific double-stranded DNA binding | 144 | 1128 | 4.86e-27 |
| GO:MF | GO:0043565 | sequence-specific DNA binding | 148 | 1220 | 3.07e-26 |
| GO:MF | GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | 130 | 935 | 1.74e-25 |
| GO:MF | GO:0003690 | double-stranded DNA binding | 145 | 1209 | 7.19e-25 |
| GO:MF | GO:0000987 | cis-regulatory region sequence-specific DNA binding | 92 | 860 | 1.13e-22 |
| GO:MF | GO:0000978 | RNA polymerase II cis-regulatory region sequence-specific DNA binding | 91 | 843 | 1.33e-22 |
| GO:MF | GO:0001217 | DNA-binding transcription repressor activity | 35 | 246 | 2.35e-07 |
| GO:MF | GO:0001228 | DNA-binding transcription activator activity, RNA polymerase II-specific | 39 | 304 | 3.92e-07 |
| GO:MF | GO:0001216 | DNA-binding transcription activator activity | 39 | 308 | 4.64e-07 |
| GO:MF | GO:0001227 | DNA-binding transcription repressor activity, RNA polymerase II-specific | 33 | 242 | 1.69e-06 |
| GO:MF | GO:0046872 | metal ion binding | 204 | 3328 | 4.40e-06 |
| GO:MF | GO:0043169 | cation binding | 204 | 3392 | 2.37e-05 |
I first looked at the data with all genes from the sigDA3 dataset. I used the list of all genes based on my rowMeans>0 filtering as background.
I then separated the VDA3 file by log2 Fold Change to see how the gene sets are enriched. Nothing showed up in the GO-BP/CC/MG-down regulated gene-set at a significant level, p<0.05.
| source | term_id | term_name | intersection_size | term_size | p_value |
|---|---|---|---|---|---|
| GO:BP | GO:0000070 | mitotic sister chromatid segregation | 74 | 192 | 8.62e-05 |
| GO:BP | GO:0000819 | sister chromatid segregation | 81 | 215 | 8.62e-05 |
| GO:BP | GO:0045930 | negative regulation of mitotic cell cycle | 83 | 212 | 8.62e-05 |
| GO:CC | GO:0098687 | chromosomal region | 126 | 353 | 2.75e-08 |
| GO:CC | GO:0000775 | chromosome, centromeric region | 89 | 229 | 2.23e-06 |
| GO:CC | GO:0000940 | outer kinetochore | 11 | 12 | 2.39e-05 |
| GO:CC | GO:0000779 | condensed chromosome, centromeric region | 64 | 167 | 4.66e-05 |
First get a list of genes you want to see. There are multiple ways to “see” these. I used the word ‘apple’ to store my list
sessionInfo()R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
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
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] scales_1.2.1 kableExtra_1.3.4 VennDiagram_1.7.3
[4] futile.logger_1.4.3 gridExtra_2.3 BiocGenerics_0.42.0
[7] forcats_1.0.0 stringr_1.5.0 dplyr_1.1.0
[10] purrr_1.0.1 readr_2.1.3 tidyr_1.3.0
[13] tibble_3.1.8 ggplot2_3.4.0 tidyverse_1.3.2
[16] gprofiler2_0.2.1 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] bitops_1.0-7 fs_1.6.0 bit64_4.0.5
[4] lubridate_1.9.1 webshot_0.5.4 httr_1.4.4
[7] rprojroot_2.0.3 tools_4.2.2 backports_1.4.1
[10] bslib_0.4.2 utf8_1.2.2 R6_2.5.1
[13] DBI_1.1.3 lazyeval_0.2.2 colorspace_2.1-0
[16] withr_2.5.0 tidyselect_1.2.0 processx_3.8.0
[19] bit_4.0.5 compiler_4.2.2 git2r_0.31.0
[22] cli_3.6.0 rvest_1.0.3 formatR_1.14
[25] xml2_1.3.3 plotly_4.10.1 labeling_0.4.2
[28] sass_0.4.5 callr_3.7.3 systemfonts_1.0.4
[31] digest_0.6.31 svglite_2.1.1 rmarkdown_2.20
[34] pkgconfig_2.0.3 htmltools_0.5.4 highr_0.10
[37] dbplyr_2.3.0 fastmap_1.1.0 htmlwidgets_1.6.1
[40] rlang_1.0.6 readxl_1.4.1 rstudioapi_0.14
[43] shiny_1.7.4 jquerylib_0.1.4 generics_0.1.3
[46] jsonlite_1.8.4 crosstalk_1.2.0 vroom_1.6.1
[49] googlesheets4_1.0.1 RCurl_1.98-1.10 magrittr_2.0.3
[52] Rcpp_1.0.10 munsell_0.5.0 fansi_1.0.4
[55] lifecycle_1.0.3 stringi_1.7.12 whisker_0.4.1
[58] yaml_2.3.7 parallel_4.2.2 promises_1.2.0.1
[61] crayon_1.5.2 haven_2.5.1 hms_1.1.2
[64] knitr_1.42 ps_1.7.2 pillar_1.8.1
[67] futile.options_1.0.1 reprex_2.0.2 glue_1.6.2
[70] evaluate_0.20 getPass_0.2-2 lambda.r_1.2.4
[73] data.table_1.14.6 modelr_0.1.10 vctrs_0.5.2
[76] tzdb_0.3.0 httpuv_1.6.8 cellranger_1.1.0
[79] gtable_0.3.1 assertthat_0.2.1 cachem_1.0.6
[82] xfun_0.36 mime_0.12 xtable_1.8-4
[85] broom_1.0.3 later_1.3.0 googledrive_2.0.0
[88] viridisLite_0.4.1 gargle_1.2.1 timechange_0.2.0
[91] ellipsis_0.3.2