• Introduction
  • Libraries and sources
  • Cross species analysis analysis
    • Translation of human genes to mouse genes
    • Correlation of mouse-human-genes
    • Top differentially expressed metabolic and carrier genes

Last updated: 2023-09-28

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Knit directory: cirrhosis-metabolism/

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Introduction

This script compares the expression of metabolic and carrier genes in mouse and human.

Libraries and sources

These libraries and sources are used for this analysis.

# data wrangling
library(tidyverse)
library(biobroom)

# statistics
library(survcomp)

# plotting
library(lemon)
library(gtools)
library(plotly)

# colors
library(AachenColorPalette)

# development helpers
library(here)
library(devtools)

# source scripts from external projects
base_url <- "https://raw.githubusercontent.com/saezlab/liver-disease-atlas"
source_url(file.path(base_url, "master", "code", "utils-plots.R"))
source_url(file.path(base_url, "master", "code", "utils-utils.R"))

Cross species analysis analysis

Translation of human genes to mouse genes

Correlation of mouse-human-genes

Version Author Date
b620f23 christianholland 2023-01-07
-0.6-0.4-0.20.00.2-2-101-0.50-0.250.000.25-2-101-0.40.00.4-2-101-0.6-0.30.00.3-2-101-0.40.00.40.8-2-101-0.50.00.5-2-101-0.50.00.51.0-2-101-1.0-0.50.00.51.0-2-1010.00.5-0.50.00.51.00.00.51.0-0.50.00.51.0-0.50.00.51.01.5-0.50.00.51.0-0.50.00.51.01.5-0.50.00.51.0-1.0-0.50.00.5-10123401-101234-0.2-0.10.00.10.2-101234-0.50-0.250.000.25-101234-0.4-0.20.00.20.4-101234-0.50-0.250.000.25-101234-0.50.00.5-101234-0.6-0.30.00.3-101234-1.0-0.50.00.5-101234-1.0-0.50.00.51.0-101234-1.0-0.50.00.51.0-101234-0.50-0.250.00-2-101-0.3-0.2-0.10.0-2-101-0.50.00.5-2024-0.3-0.2-0.10.00.10.2-2024-0.4-0.20.00.20.4-2024
sigBoth speciesMouse onlyHuman onlyNeither human nor mouseMissing human dataHuman logFCMouse logFCADH/ALDHnafld_vs_ctrl | omni | hampe14ADH/ALDHnash_vs_ctrl | omni | hampe14ADH/ALDHstage_1_vs_0 | nafld | hoangADH/ALDHstage_2_vs_0 | nafld | hoangADH/ALDHstage_3_vs_0 | nafld | hoangADH/ALDHstage_4_vs_0 | nafld | hoangADH/ALDHstage_5_vs_0 | nafld | hoangADH/ALDHstage_6_vs_0 | nafld | hoangDHstage_3_vs_0 | nafld | hoangDHstage_4_vs_0 | nafld | hoangDHstage_5_vs_0 | nafld | hoangDHstage_6_vs_0 | nafld | hoangMThcv_adv_vs_early | fibrosis | ramnathMTnafld_adv_vs_early | fibrosis | ramnathMTnafld_vs_ctrl | omni | hampe14MTnash_vs_ctrl | nash | hampe13MTnash_vs_ctrl | omni | hampe14MTpbc_vs_ctrl | omni | hampe14MTstage_2_vs_0 | nafld | hoangMTstage_3_vs_0 | nafld | hoangMTstage_4_vs_0 | nafld | hoangMTstage_5_vs_0 | nafld | hoangMTstage_6_vs_0 | nafld | hoangNAThcv_adv_vs_early | fibrosis | ramnathNATnash_vs_ctrl | omni | hampe14Bloodhcv_adv_vs_early | fibrosis | ramnathBloodstage_1_vs_0 | nafld | hoangBloodstage_4_vs_0 | nafld | hoang

Top differentially expressed metabolic and carrier genes

Version Author Date
4323bde christianholland 2023-01-08 

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] devtools_2.4.5.9000      usethis_2.1.6            here_1.0.1              
 [4] AachenColorPalette_1.1.3 plotly_4.10.0            gtools_3.9.4            
 [7] lemon_0.4.5              survcomp_1.46.0          prodlim_2019.11.13      
[10] survival_3.3-1           biobroom_1.28.0          broom_1.0.1             
[13] forcats_0.5.2            stringr_1.4.1            dplyr_1.0.10            
[16] purrr_0.3.5              readr_2.1.3              tidyr_1.2.1             
[19] tibble_3.1.8             ggplot2_3.3.6            tidyverse_1.3.2         
[22] workflowr_1.7.0         

loaded via a namespace (and not attached):
  [1] googledrive_2.0.0   colorspace_2.0-3    ellipsis_0.3.2     
  [4] rprojroot_2.0.3     fs_1.5.2            rstudioapi_0.14    
  [7] farver_2.1.1        listenv_0.8.0       remotes_2.4.2      
 [10] fansi_1.0.3         lubridate_1.8.0     xml2_1.3.3         
 [13] codetools_0.2-18    splines_4.2.1       cachem_1.0.6       
 [16] knitr_1.40          SuppDists_1.1-9.7   pkgload_1.3.0      
 [19] jsonlite_1.8.3      dbplyr_2.2.1        shiny_1.7.2        
 [22] compiler_4.2.1      httr_1.4.4          backports_1.4.1    
 [25] assertthat_0.2.1    Matrix_1.4-1        fastmap_1.1.0      
 [28] lazyeval_0.2.2      gargle_1.2.1        cli_3.4.1          
 [31] later_1.3.0         prettyunits_1.1.1   htmltools_0.5.3    
 [34] tools_4.2.1         gtable_0.3.1        glue_1.6.2         
 [37] Rcpp_1.0.9          Biobase_2.56.0      cellranger_1.1.0   
 [40] jquerylib_0.1.4     vctrs_0.5.0         nlme_3.1-157       
 [43] crosstalk_1.2.0     xfun_0.34           globals_0.16.2     
 [46] ps_1.7.1            rvest_1.0.3         mime_0.12          
 [49] miniUI_0.1.1.1      lifecycle_1.0.3     renv_0.16.0        
 [52] googlesheets4_1.0.1 future_1.29.0       getPass_0.2-2      
 [55] scales_1.2.1        hms_1.1.2           promises_1.2.0.1   
 [58] parallel_4.2.1      curl_4.3.3          yaml_2.3.6         
 [61] memoise_2.0.1       gridExtra_2.3       sass_0.4.2         
 [64] stringi_1.7.8       rmeta_3.0           highr_0.9          
 [67] BiocGenerics_0.42.0 pkgbuild_1.3.1      lava_1.7.0         
 [70] rlang_1.0.6         pkgconfig_2.0.3     evaluate_0.17      
 [73] lattice_0.20-45     labeling_0.4.2      htmlwidgets_1.5.4  
 [76] survivalROC_1.0.3.1 cowplot_1.1.1       processx_3.7.0     
 [79] tidyselect_1.2.0    parallelly_1.32.1   plyr_1.8.7         
 [82] magrittr_2.0.3      R6_2.5.1            profvis_0.3.7      
 [85] generics_0.1.3      bootstrap_2019.6    DBI_1.1.3          
 [88] mgcv_1.8-40         pillar_1.8.1        haven_2.5.1        
 [91] whisker_0.4         withr_2.5.0         future.apply_1.10.0
 [94] modelr_0.1.9        crayon_1.5.2        KernSmooth_2.23-20 
 [97] utf8_1.2.2          urlchecker_1.0.1    tzdb_0.3.0         
[100] rmarkdown_2.17      grid_4.2.1          readxl_1.4.1       
[103] data.table_1.14.4   callr_3.7.2         git2r_0.30.1       
[106] reprex_2.0.2        digest_0.6.30       xtable_1.8-4       
[109] httpuv_1.6.6        munsell_0.5.0       viridisLite_0.4.1  
[112] bslib_0.4.0         sessioninfo_1.2.2