Viper
Last updated: 2024-05-21
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Knit directory: PPP/
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| html | 3e0915c | Zhen Zuo | 2024-05-21 | Build site. |
| html | 68d3a8b | Zhen Zuo | 2024-05-21 | Build site. |
| Rmd | e4c8a72 | Zhen Zuo | 2024-05-21 | wflow_publish(all = TRUE) |
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| html | a8e0d13 | Zhen Zuo | 2024-05-21 | Build site. |
| Rmd | 1bb174f | Zhen Zuo | 2024-05-21 | Publish the initial files for myproject |
Load packages
library(viper)
library(aracne.networks)Context-specific networks
print(data(package="aracne.networks")$results[, "Item"]) [1] "regulonblca" "regulonbrca" "reguloncesc" "reguloncoad" "regulonesca"
[6] "regulongbm" "regulonhnsc" "regulonkirc" "regulonkirp" "regulonlaml"
[11] "regulonlihc" "regulonluad" "regulonlusc" "regulonnet" "regulonov"
[16] "regulonpaad" "regulonpcpg" "regulonprad" "regulonread" "regulonsarc"
[21] "regulonstad" "regulontgct" "regulonthca" "regulonthym" "regulonucec"df <- read.csv("data/aracne.networks.csv")
knitr::kable(df)| regulon | description |
|---|---|
| regulonblca | Human Bladder Carcinoma context-specific ARACNe interactome |
| regulonbrca | Human Breast Carcinoma context-specific ARACNe interactome |
| reguloncesc | Human Cervical Squamous Carcinoma context-specific ARACNe interactome |
| reguloncoad | Human Colon Adenocarcinoma context-specific ARACNe interactome |
| regulonesca | Human Esophageal Carcinoma context-specific ARACNe interactome |
| regulongbm | Human Glioblastoma context-specific ARACNe interactome |
| regulonhnsc | Human Head and Neck Squamous Carcinoma context-specific ARACNe interactome |
| regulonkirc | Human Kidney Renal Clear Cell Carcinoma context-specific ARACNe interactome |
| regulonkirp | Human Kidney Papillary Carcinoma context-specific ARACNe interactome |
| regulonlaml | Human Acute Myeloid Leukemia context-specific ARACNe interactome |
| regulonlihc | Human Liver Hepatocellular Carcinoma context-specific ARACNe interactome |
| regulonluad | Human Lung Adenocarcinoma context-specific ARACNe interactome |
| regulonlusc | Human Lung Squamous Carcinoma context-specific ARACNe interactome |
| regulonnet | Human Neuroendocrine tumor context-specific ARACNe interactome |
| regulonov | Human Ovarian Carcinoma context-specific ARACNe interactome |
| regulonpaad | Human Pancreas Carcinoma context-specific ARACNe interactome |
| regulonpcpg | Human Pheochromocytoma and Paraganglioma context-specific ARACNe interactome |
| regulonprad | Human Prostate Carcinoma context-specific ARACNe interactome |
| regulonread | Human Rectal Adenocarcinoma context-specific ARACNe interactome |
| regulonsarc | Human Sarcoma context-specific ARACNe interactome |
| regulonstad | Human Stomach Adenocarcinoma context-specific ARACNe interactome |
| regulontgct | Human Testicular Cancer context-specific ARACNe interactome |
| regulonthca | Human Thyroid Carcinoma context-specific ARACNe interactome |
| regulonthym | Human Thymoma context-specific ARACNe interactome |
| regulonucec | Human Utherine Corpus Endometroid Carcinoma context-specific ARACNe interactome |
data(bcellViper, package="bcellViper")
adjfile <- system.file("aracne", "bcellaracne.adj", package = "bcellViper")
regul <- aracne2regulon(adjfile, dset, verbose = FALSE)number of iterations= 301 signature <- rowTtest(dset, "description", c("CB", "CC"), "N")signature <- (qnorm(signature$p.value/2, lower.tail = FALSE) * + sign(signature$statistic))[, 1]nullmodel <- ttestNull(dset, "description", c("CB", "CC"), "N", per = 1000, repos = TRUE, verbose = FALSE)mrs <- msviper(signature, regulon, nullmodel, verbose = FALSE)summary(mrs) Regulon Size NES p.value FDR
TCF3 TCF3 298 3.30 0.000962 0.028
BCL6 BCL6 401 3.28 0.001030 0.028
KLF10 KLF10 254 3.25 0.001170 0.028
MYBL2 MYBL2 240 3.22 0.001300 0.028
TSC22D3 TSC22D3 333 -3.17 0.001520 0.028
HES1 HES1 360 -3.18 0.001470 0.028
ZNF32 ZNF32 291 -3.19 0.001420 0.028
ZMYND11 ZMYND11 452 -3.20 0.001380 0.028
ZNF101 ZNF101 301 -3.22 0.001300 0.028
KLF9 KLF9 337 -3.24 0.001190 0.028plot(mrs, cex = .7)
| Version | Author | Date |
|---|---|---|
| 68d3a8b | Zhen Zuo | 2024-05-21 |
mrs <- ledge(mrs)
summary(mrs) Regulon Size NES p.value FDR
TCF3 TCF3 298 3.30 0.000962 0.028
BCL6 BCL6 401 3.28 0.001030 0.028
KLF10 KLF10 254 3.25 0.001170 0.028
MYBL2 MYBL2 240 3.22 0.001300 0.028
TSC22D3 TSC22D3 333 -3.17 0.001520 0.028
HES1 HES1 360 -3.18 0.001470 0.028
ZNF32 ZNF32 291 -3.19 0.001420 0.028
ZMYND11 ZMYND11 452 -3.20 0.001380 0.028
ZNF101 ZNF101 301 -3.22 0.001300 0.028
KLF9 KLF9 337 -3.24 0.001190 0.028
Ledge
TCF3 SMARCA4, MCM7, TRAF3IP3, NDC80, + 110 genes
BCL6 KIF14, BUB1, DLGAP4, GINS1, + 217 genes
KLF10 TRIP13, NDC80, AHNAK, KIF2C, + 99 genes
MYBL2 SMARCA4, MCM7, TRIP13, GINS1, + 138 genes
TSC22D3 NOTCH2, RAD1, RBM19, MLEC, + 190 genes
HES1 CDK4, SHC1, STX7, MAN1A1, + 104 genes
ZNF32 GNA12, PLAG1, PSMB1, CARM1, + 145 genes
ZMYND11 ANKRD26, EXTL2, IGFBP4, CTSC, + 234 genes
ZNF101 SLC46A3, GCLM, TCEA2, HMOX2, + 128 genes
KLF9 IFIT1, LPAR1, NID1, STOM, + 158 genessignature <- bootstrapTtest(dset, "description", c("CB", "CC"), "N", verbose = FALSE)
mrs <- msviper(signature, regulon, nullmodel, verbose = FALSE)
mrs <- bootstrapmsviper(mrs, "mode")
plot(mrs, cex = .7)
| Version | Author | Date |
|---|---|---|
| 68d3a8b | Zhen Zuo | 2024-05-21 |
mrshadow <- shadow(mrs, regulators = 25, verbose = FALSE)
summary(mrshadow)$msviper.results
Regulon Size NES p.value FDR
BCL6 BCL6 401 3.18 0.00146 0.0709
MYBL2 MYBL2 240 3.12 0.00184 0.0709
WHSC1 WHSC1 257 3.07 0.00213 0.0709
TOP2A TOP2A 749 3.06 0.00222 0.0709
MYBL1 MYBL1 225 3.04 0.00239 0.0709
PTTG1 PTTG1 471 3.00 0.00273 0.0709
NR1D2 NR1D2 259 -3.00 0.00266 0.0709
TSC22D3 TSC22D3 313 -3.02 0.00255 0.0709
ZNF274 ZNF274 160 -3.04 0.00235 0.0709
ZMYND11 ZMYND11 452 -3.06 0.00220 0.0709
$Shadow.pairs
[1] "BCL6 -> TCF3" "BCL6 -> HES1" "MYBL2 -> ZNF32"
[4] "MYBL2 -> HES1" "MYBL2 -> ZNF23" "MYBL2 -> MEIS2"
[7] "KLF10 -> ZNF101" "KLF10 -> HES1" "KLF9 -> HES1"
[10] "ZNF32 -> HES1" "WHSC1 -> TSC22D3" "WHSC1 -> ZNF101"
[13] "WHSC1 -> IRF5" "WHSC1 -> KDM1A" "WHSC1 -> E2F2"
[16] "TSC22D3 -> HES1" "TSC22D3 -> ZNF23" "TOP2A -> CREB3L2"
[19] "TOP2A -> E2F2" "TOP2A -> HES1" "TOP2A -> HMGB2"
[22] "TOP2A -> MEIS2" "ZMYND11 -> IRF5" "ZMYND11 -> E2F2"
[25] "ZMYND11 -> HES1" "ZMYND11 -> MEIS2" "CREB3L2 -> E2F2"
[28] "PRKDC -> HES1" "IRF5 -> HES1" "PTTG1 -> E2F2"
[31] "ZNF274 -> E2F2" "ZNF274 -> ZNF23" "ZNF274 -> MEIS2"
[34] "NR1D2 -> HES1" "NR1D2 -> HMGB2" "HES1 -> HMGB2"
[37] "WHSC1 -> KLF10" "TSC22D3 -> KLF10" "PRKDC -> KLF10"
[40] "ZNF274 -> KLF10" "KDM1A -> KLF10" "ZNF23 -> KLF10"
[43] "HMGB2 -> KLF10" "MEIS2 -> KLF10" "ZNF32 -> KLF9"
[46] "PRKDC -> KLF9" "MYBL1 -> KLF9" "IRF5 -> KLF9"
[49] "ZNF274 -> KLF9" "WHSC1 -> ZNF32" "TSC22D3 -> ZNF32"
[52] "KDM1A -> ZNF32" "HMGB2 -> ZNF32" "PRKDC -> TCF3"
[55] "MYBL1 -> TCF3" "IRF5 -> TCF3" "PTTG1 -> TCF3"
[58] "KDM1A -> TCF3" "HMGB2 -> TCF3" "TOP2A -> ZNF101"
[61] "PRKDC -> ZNF101" "MYBL1 -> ZNF101" "PTTG1 -> ZNF101"
[64] "ZNF274 -> ZNF101" "NR1D2 -> ZNF101" "PTTG1 -> CREB3L2"
[67] "ZNF274 -> CREB3L2" "HMGB2 -> CREB3L2" "MYBL1 -> PRKDC"
[70] "HMGB2 -> MYBL1" "ZNF274 -> PTTG1" "HMGB2 -> KDM1A"
[73] "NR1D2 -> E2F2"
sessionInfo()R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aracne.networks_1.30.0 viper_1.38.0 Biobase_2.64.0
[4] BiocGenerics_0.50.0
loaded via a namespace (and not attached):
[1] gtable_0.3.5 xfun_0.44 bslib_0.7.0 ggplot2_3.5.1
[5] htmlwidgets_1.6.4 lattice_0.22-6 vctrs_0.6.5 tools_4.4.0
[9] generics_0.1.3 parallel_4.4.0 tibble_3.2.1 proxy_0.4-27
[13] fansi_1.0.6 highr_0.10 pkgconfig_2.0.3 Matrix_1.7-0
[17] KernSmooth_2.23-24 data.table_1.15.4 lifecycle_1.0.4 compiler_4.4.0
[21] stringr_1.5.1 git2r_0.33.0 mixtools_2.0.0 munsell_0.5.1
[25] httpuv_1.6.15 htmltools_0.5.8.1 class_7.3-22 sass_0.4.9
[29] yaml_2.3.8 lazyeval_0.2.2 plotly_4.10.4 later_1.3.2
[33] pillar_1.9.0 jquerylib_0.1.4 whisker_0.4.1 tidyr_1.3.1
[37] MASS_7.3-60.2 cachem_1.1.0 nlme_3.1-164 tidyselect_1.2.1
[41] digest_0.6.35 stringi_1.8.4 kernlab_0.9-32 dplyr_1.1.4
[45] purrr_1.0.2 splines_4.4.0 rprojroot_2.0.4 fastmap_1.2.0
[49] grid_4.4.0 colorspace_2.1-0 cli_3.6.2 magrittr_2.0.3
[53] survival_3.6-4 utf8_1.2.4 e1071_1.7-14 scales_1.3.0
[57] promises_1.3.0 segmented_2.1-0 rmarkdown_2.27 httr_1.4.7
[61] workflowr_1.7.1 evaluate_0.23 knitr_1.46 viridisLite_0.4.2
[65] rlang_1.1.3 Rcpp_1.0.12 glue_1.7.0 rstudioapi_0.16.0
[69] jsonlite_1.8.8 R6_2.5.1 fs_1.6.4