Abstract
‘deplink’ compares the genetic/epigenetic features between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Install deplink
Load deplink and data libraries
All-in-one analysis
For example, deplink compares the genetic/epigenetic features between cancer cell lines with highest and lowest dependencies of “9-1-1” complex members:
The results will be output to a local directory (default: root directory) under a folder in name of the designated “signature.name” (“9-1-1” in this case).
Several cutoffs are set by default as below and can be changed by will. Please see the help page for more details (?deplink).
cutoff.freq = 10
cutoff.percentile = 0.2
cutoff.pvalue = 0.05
cutoff.qvalue = 0.1
cutoff.diff = 0.1
cutoff.fc = 2
The comparison covers the following features:
- Genomic/epigenetic features
- Genetic dependency
- Gene expression
- Chromatin modification
- Genome instability
- Genetic mutation
- COSMIC signature
- Tumor mutation burden (TMB)
- Copy number variation (CNV)
- Microsatellite instability (MSI)
- Drug sensitivity
- Drug sensitivity from GDSC data set
- Drug sensitivity from PRISM data set
- Immune infiltration
- Immune signature gene (ISG)
- Stemness
- mRNA stemness index (mRNAsi)
- Epithelial–mesenchymal transition (EMT)
- Misc.
- Cancer type
Individual analysis
deplink can compare individual genetic/epigenetic feature between cancer cell lines with highest and lowest dependencies of a gene set (signature). For example of “9-1-1” complex members:
## "9-1-1" complex members as a gene set (signature)
signature.name = "9-1-1"
signature = c("RAD9A", "RAD1", "HUS1", "RAD17")
Cancer type component
‘cancertypeHigh’ displays the cancer type component of cell lines with high dependencies of a gene set (signature).
## display the cancer type component of cell lines with high dependencies of "9-1-1" complex
cancertypeHigh(signature.name, signature)
‘cancertypeLow’ displays the cancer type component of cell lines with low dependencies of a gene set (signature).
## display the cancer type component of cell lines with low dependencies of "9-1-1" complex
cancertypeLow(signature.name, signature)
‘cancertypeLandscape’ displays the landscape of cancer type component of cell lines with different dependencies of a gene set (signature).
Genetic dependency
‘dependency’ compares the genetic dependency between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Gene expression
‘expressions’ compares the gene expression between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Chromatin modification
‘chromatinModification’ compares the chromatin modification abundance between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Genetic mutation
‘mutations’ compares the genetic mutations between cancer cell lines with highest and lowest dependencies of a gene set (signature).
COSMIC signature
‘cosmic’ compares the COSMIC signatures between cell lines with highest and lowest dependencies of a gene set (signature).
Tumor mutation burden (TMB)
‘tmb’ compares the tumor mutation burden (TMB) between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Copy number variation (CNV)
‘cnv’ compares the copy number variation (CNV) between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Microsatellite instability (MSI)
‘msi’ compares the microsatellite instability (MSI) between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Drug sensitivity
‘drugGDSC’ compares the drug sensitivity (GDSC dataset) between cancer cell lines with highest and lowest dependencies of a gene set (signature).
## compare the drug sensitivity (GDSC dataset) between cancer cell lines with highest and lowest dependencies of "9-1-1" complex
drugGDSC(signature.name, signature)
‘drugPRISM’ compares the drug sensitivity (PRISM dataset) between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Immune signature gene (ISG)
‘isg’ compares the immune signature gene (ISG) between cancer cell lines with highest and lowest dependencies of a gene set (signature).
mRNA stemness index (mRNAsi)
‘mrnasi’ compares the mRNA stemness index (mRNAsi) between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Epithelial–mesenchymal transition (EMT)
‘emt’ compares the epithelial–mesenchymal transition (EMT) between cancer cell lines with highest and lowest dependencies of a gene set (signature).
Citation
If you use deplink in published research, please cite the most appropriate paper(s) from this list:
- X Chen, J McGuire, F Zhu, X Xu, Y Li, D Karagiannis, R Dalla-Favera, A Ciccia, J Amengual & C Lu (2020). Harnessing genetic dependency correlation network to reveal chromatin vulnerability in cancer. In preparation.
Session Information
Here is the output of sessionInfo()
on the system on which this document was compiled:
## R version 3.5.0 (2018-04-23)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 17134)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United States.1252
## [2] LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] deplink_0.99.0 wesanderson_0.3.6 purrr_0.3.4 ggrepel_0.8.2
## [5] ggpubr_0.2.5 magrittr_1.5 ggplot2_3.3.0 data.table_1.12.8
## [9] cowplot_1.0.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.18 pillar_1.3.0 compiler_3.5.0 bindr_0.1.1
## [5] prettydoc_0.4.0 tools_3.5.0 digest_0.6.18 evaluate_0.14
## [9] tibble_1.4.2 gtable_0.2.0 pkgconfig_2.0.2 rlang_0.4.5
## [13] yaml_2.2.0 xfun_0.17 bindrcpp_0.2.2 withr_2.1.2
## [17] dplyr_0.7.6 stringr_1.3.1 knitr_1.23 grid_3.5.0
## [21] tidyselect_0.2.5 glue_1.3.0 R6_2.2.2 rmarkdown_2.3
## [25] scales_1.0.0 htmltools_0.3.6 assertthat_0.2.0 colorspace_1.3-2
## [29] ggsignif_0.4.0 labeling_0.3 stringi_1.2.4 munsell_0.5.0
## [33] crayon_1.3.4