Introduction

This dataset contains nine tissues (heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen) from C57BL/6J mice that were fed 2-deoxyglucose (6g/L) through their drinking water for 96hrs or 4wks. 96hr mice were given their 2DG treatment 2 weeks after the other cohort started the 4 week treatment. The organs from the mice were harvested and processed for metabolomics and transcriptomics. The data in this document pertains to the transcriptomics data only. The counts that were used were FPKM normalized before being log transformed. It was determined that sample A113 had low RNAseq quality and through further analyses with PCA, MA plots, and clustering was an outlier and will be removed for the rest of the analyses performed. This document will assess the number of genes that are shared between tissue modules of interest.

needed.packages <- c("tidyverse", "here", "functional", "gplots", "dplyr", "GeneOverlap", "R.utils", "reshape2","magrittr","data.table", "RColorBrewer","preprocessCore", "ARTool","emmeans", "phia", "gprofiler2","rlist", "plotly","kableExtra","foreach","doParallel","doFuture","UpSetR")
for(i in 1:length(needed.packages)){library(needed.packages[i], character.only = TRUE)}

source(here("source_files","WGCNA_source.R"))
heart <- readRDS(here("Data","Heart","log.tdata.FPKM.sample.info.subset.heart.WGCNA.module.membership.RData"))

small.intestine <- readRDS(here("Data","Small Intestine", "log.tdata.FPKM.sample.info.subset.small.intestine.WGCNA.module.membership.RData"))

spleen <- readRDS(here("Data","Spleen","log.tdata.FPKM.sample.info.subset.spleen.WGCNA.module.membership.RData"))

brain <- readRDS(here("Data","Brain","log.tdata.FPKM.sample.info.subset.hip.hyp.cortex.WGCNA.module.membership.RData"))

muscle <- readRDS(here("Data","Skeletal Muscle","log.tdata.FPKM.sample.info.subset.skeletal.muscle.WGCNA.module.membership.RData"))

liver <- readRDS(here("Data","Liver","log.tdata.FPKM.sample.info.subset.liver.WGCNA.module.membership.RData"))

hyp <- readRDS(here("Data","Hypothalamus","log.tdata.FPKM.sample.info.subset.hypothalamus.WGCNA.module.membership.RData"))

cortex <- readRDS(here("Data","Prefrontal Cortex","log.tdata.FPKM.sample.info.subset.prefrontal.cortex.WGCNA.module.membership.RData"))

Upset Plots

## heart
Matched.module.heart <- split(heart$Gene, heart$Module)

modulenames <- c()
  for(i in 1:length(Matched.module.heart)){
    modules <- unique(heart$Module)
    name <- str_split(modules,"_")
    modulenames[i] <- name[[i]][2]
    
    #gene <- as.vector(Matched.module[[i]])
  }

modulenames <- sort(modulenames)

names(Matched.module.heart) <- modulenames

## small intestine
Matched.module.SI <- split(small.intestine$Gene, small.intestine$Module)

modulenames <- c()
  for(i in 1:length(Matched.module.SI)){
    modules <- unique(small.intestine$Module)
    name <- str_split(modules,"_")
    modulenames[i] <- name[[i]][2]
    
    #gene <- as.vector(Matched.module[[i]])
  }

modulenames <- sort(modulenames)

names(Matched.module.SI) <- modulenames

## skeletal muscle
Matched.module.SM <- split(muscle$Gene, muscle$Module)

modulenames <- c()
  for(i in 1:length(Matched.module.SM)){
    modules <- unique(muscle$Module)
    name <- str_split(modules,"_")
    modulenames[i] <- name[[i]][2]
    
    #gene <- as.vector(Matched.module[[i]])
  }

modulenames <- sort(modulenames)

names(Matched.module.SM) <- modulenames

## liver
Matched.module.liver <- split(liver$Gene, liver$Module)

modulenames <- c()
  for(i in 1:length(Matched.module.liver)){
    modules <- unique(liver$Module)
    name <- str_split(modules,"_")
    modulenames[i] <- name[[i]][2]
    
    #gene <- as.vector(Matched.module[[i]])
  }

modulenames <- sort(modulenames)

names(Matched.module.liver) <- modulenames

## hypothalamus
Matched.module.hyp <- split(hyp$Gene, hyp$Module)

modulenames <- c()
  for(i in 1:length(Matched.module.hyp)){
    modules <- unique(hyp$Module)
    name <- str_split(modules,"_")
    modulenames[i] <- name[[i]][2]
    
    #gene <- as.vector(Matched.module[[i]])
  }

modulenames <- sort(modulenames)

names(Matched.module.hyp) <- modulenames

## prefrontal cortex
Matched.module.cortex <- split(cortex$Gene, cortex$Module)

modulenames <- c()
  for(i in 1:length(Matched.module.cortex)){
    modules <- unique(cortex$Module)
    name <- str_split(modules,"_")
    modulenames[i] <- name[[i]][2]
    
    #gene <- as.vector(Matched.module[[i]])
  }

modulenames <- sort(modulenames)

names(Matched.module.cortex) <- modulenames

With Brain

tissues.treat <- list("Heart" = Matched.module.heart$darkgreen, "Hypothalamus" = Matched.module.hyp$bisque4, "Liver" = Matched.module.liver$darkolivegreen, "Prefrontal Cortex" = Matched.module.cortex$bisque2, "Skeletal Muscle" = Matched.module.SM$salmon2, "Small Intestine" = Matched.module.SI$green4)

upset(nsets=6, fromList(tissues.treat), main.bar.color = "salmon", matrix.color = "midnightblue", sets.bar.color = "darkolivegreen", text.scale = 1)

Without Brain

tissues.treat.nobrain <- list("Heart" = Matched.module.heart$darkgreen, "Liver" = Matched.module.liver$darkolivegreen, "Skeletal Muscle" = Matched.module.SM$salmon2, "Small Intestine" = Matched.module.SI$green4)

upset(nsets=, fromList(tissues.treat.nobrain), main.bar.color = "salmon", matrix.color = "midnightblue", sets.bar.color = "darkolivegreen", text.scale = 1)

Pathways

heart <- readRDS(here("Data","Heart","Chang_B6_96hr_4wk_gprofiler_pathway_annotation_list_heart_WGCNA.RData"))
names(heart) <- as.list(names(Matched.module.heart))

hyp <- readRDS(here("Data","Hypothalamus","Chang_B6_96hr_4wk_gprofiler_pathway_annotation_list_hypothalamus_WGCNA.RData"))
names(hyp) <- as.list(names(Matched.module.hyp))

liver <- readRDS(here("Data","Liver","Chang_B6_96hr_4wk_gprofiler_pathway_annotation_list_liver_WGCNA.RData"))
names(liver) <- as.list(names(Matched.module.liver))

cortex <- readRDS(here("Data","Prefrontal Cortex","Chang_B6_96hr_4wk_gprofiler_pathway_annotation_list_prefrontal_cortex_WGCNA.RData"))
names(cortex) <- as.list(names(Matched.module.cortex))

muscle <- readRDS(here("Data","Skeletal Muscle","Chang_B6_96hr_4wk_gprofiler_pathway_annotation_list_skeletal_muscle_WGCNA.RData"))
names(muscle) <- as.list(names(Matched.module.SM))

small.intestine <- readRDS(here("Data","Small Intestine","Chang_B6_96hr_4wk_gprofiler_pathway_annotation_list_small_intestine_WGCNA.RData"))
names(small.intestine) <- as.list(names(Matched.module.SI))

Treatment

treat <- list("Heart" = heart$darkgreen$term_name, "Hypothalamus" = hyp$bisque4$term_name, "Liver" = liver$darkolivegreen$term_name, "Prefrontal Cortex" = cortex$bisque2$term_name, "Skeletal Muscle" = muscle$salmon2$term_name, "Small Intestine" = small.intestine$green4$term_name)

upset(nsets=6, fromList(treat), main.bar.color = "darkolivegreen4", matrix.color = "darkorchid4", sets.bar.color = "dodgerblue4", text.scale = 1)

Analysis performed by Ann Wells

The Carter Lab The Jackson Laboratory 2023

ann.wells@jax.org