Introduction and Data files

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 determine the contribution of each main effect or their combination to each module identified, as well as the relationship of each gene within the module and its significance.

needed.packages <- c("tidyverse", "here", "functional", "gplots", "dplyr", "GeneOverlap", "R.utils", "reshape2","magrittr","data.table", "RColorBrewer","preprocessCore", "ARTool","emmeans", "phia", "gProfileR", "WGCNA","plotly", "pheatmap","ppcor", "pander","downloadthis")
for(i in 1:length(needed.packages)){library(needed.packages[i], character.only = TRUE)}

source(here("source_files","WGCNA_source.R"))
source(here("source_files","WGCNA_contribution_source.R"))
tdata.FPKM.sample.info <- readRDS(here("Data","20190406_RNAseq_B6_4wk_2DG_counts_phenotypes.RData"))

tdata.FPKM <- readRDS(here("Data","20190406_RNAseq_B6_4wk_2DG_counts_numeric.RData"))

log.tdata.FPKM <- log(tdata.FPKM + 1)
log.tdata.FPKM <- as.data.frame(log.tdata.FPKM)

log.tdata.FPKM.sample.info <- cbind(log.tdata.FPKM, tdata.FPKM.sample.info[,27238:27240])

log.tdata.FPKM.sample.info <- log.tdata.FPKM.sample.info %>% rownames_to_column() %>% filter(rowname != "A113") %>% column_to_rownames()

log.tdata.FPKM.subset <- log.tdata.FPKM[,colMeans(log.tdata.FPKM != 0) > 0.5] 

log.tdata.FPKM.subset <- log.tdata.FPKM.subset %>% rownames_to_column() %>% filter(rowname != "A113") %>% column_to_rownames()

log.tdata.FPKM.sample.info.subset.hip.hypo.cortex <- log.tdata.FPKM.sample.info %>% rownames_to_column() %>% filter(Tissue %in% c("Hippocampus","Hypothanamus","Pre-frontal Cortex")) %>% column_to_rownames()

log.tdata.FPKM.subset <- subset(log.tdata.FPKM.sample.info.subset.hip.hypo.cortex, select = -c(Time,Treatment,Tissue))
  
WGCNA.pathway <-readRDS(here("Data","Brain","Chang_B6_96hr_4wk_gprofiler_pathway_annotation_list_hip_hyp_cortex_WGCNA.RData"))

Matched<-readRDS(here("Data","Brain","Annotated_genes_in_hip_hyp_cortex_WGCNA_Chang_B6_96hr_4wk.RData"))


module.names <- Matched$X..Module.
name <- str_split(module.names,"_")
samples <-c()
for(i in 1:length(name)){
samples[[i]] <- name[[i]][2]
}  
name <- str_split(samples,"\"")
name <- unlist(name)

Treatment <- unclass(as.factor(log.tdata.FPKM.sample.info.subset.hip.hypo.cortex[,27238]))
Tissue <- unclass(as.factor(log.tdata.FPKM.sample.info.subset.hip.hypo.cortex[,27239]))
Time <- unclass(as.factor(log.tdata.FPKM.sample.info.subset.hip.hypo.cortex[,27237]))
Treat.Tissue <- paste0(Treatment,Tissue)
Treat.Time <- paste0(Treatment, Time)
Tissue.Time <- paste0(Tissue, Time)
Treat.Tissue.Time <- paste0(Treatment,Tissue, Time)
phenotype <- data.frame(cbind(Tissue, Treatment, Time, Treat.Tissue, Treat.Time, Tissue.Time, Treat.Tissue.Time))

nSamples <- nrow(log.tdata.FPKM.sample.info.subset.hip.hypo.cortex)

MEs0 <- read.csv(here("Data","Brain","log.tdata.FPKM.sample.info.subset.hip.hyp.cortex.WGCNA.module.eigens.csv"),header = T, row.names = 1)
name <- str_split(names(MEs0),"_")
samples <-c()
for(i in 1:length(name)){
samples[[i]] <- name[[i]][2]
}  
name <- str_split(samples,"\"")
name <- unlist(name)
colnames(MEs0) <-name
MEs <- orderMEs(MEs0)
moduleTraitCor <- cor(MEs, phenotype, use = "p");
moduleTraitPvalue <- corPvalueStudent(moduleTraitCor, nSamples)

Relationship between Modules and Traits

#sizeGrWindow(10,6)
# Will display correlations and their p-values
textMatrix = paste(signif(moduleTraitCor, 2), "\n(",
                        signif(moduleTraitPvalue, 1), ")", sep = "");
dim(textMatrix) = dim(moduleTraitCor)

# Display the correlation values within a heatmap plot
heat <- pheatmap(moduleTraitCor, main = paste("Module-trait relationships"), display_numbers = textMatrix,color=colorRampPalette(brewer.pal(n = 12, name = "Paired"))(10), cluster_rows = F, cluster_cols = F, fontsize_number = 4, angle_col = 45, number_color = "black", border_color = "white")
heat

DT::datatable(moduleTraitPvalue, extensions = 'Buttons',
                  rownames = TRUE, 
                  filter="top",
                  options = list(dom = 'Blfrtip',
                                 buttons = c('copy', 'csv', 'excel'),
                                 lengthMenu = list(c(10,25,50,-1),
                                                   c(10,25,50,"All")), 
                                 scrollX= TRUE), class = "display")

Partial Correlation

phenotype$Tissue <- as.numeric(phenotype$Tissue)
phenotype$Treatment <- as.numeric(phenotype$Treatment)
phenotype$Time <- as.numeric(phenotype$Time)
phenotype$Treat.Tissue <- as.numeric(phenotype$Treat.Tissue)
phenotype$Treat.Time <- as.numeric(phenotype$Treat.Time)
phenotype$Tissue.Time <- as.numeric(phenotype$Tissue.Time)
phenotype$Treat.Tissue.Time <- as.numeric(phenotype$Treat.Tissue.Time)

Sigmodules <- as.data.frame(cbind(MEs$lavenderblush3,MEs$darkslateblue,MEs$chocolate3,MEs$royalblue))
colnames(Sigmodules) <- c("lavenderblush3","darkslateblue","chocolate3","royalblue")


for(i in 1:length(Sigmodules)){
   cat("\n##",colnames(Sigmodules[i]),"{.tabset .tabset-fade .tabset-pills}","\n")
   for(j in 1:length(phenotype)){
      cat("\n###", colnames(phenotype[j]),"{.tabset .tabset-fade .tabset-pills}","\n")
      for(k in 1:length(phenotype)){
         cat("\n####", "Partial Correlation", colnames(phenotype[k]),"\n")
         partial <- pcor.test(Sigmodules[,i], phenotype[,j],phenotype[,k])
         panderOptions('knitr.auto.asis', FALSE)
         print(pander(partial))
         cat("\n \n")
      }
      cat("\n \n")
   }
   cat("\n \n")
}

lavenderblush3

Tissue

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.8905 5.374e-17 -13.13 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.8945 2.429e-17 -13.42 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.8905 5.369e-17 -13.13 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.8889 7.313e-17 -13.02 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.8945 2.435e-17 -13.42 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.1118 0.4542 -0.755 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.8889 7.31e-17 -13.02 48 1 pearson

NULL

Treatment

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.2076 0.1614 -1.424 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.09447 0.5276 -0.6365 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.09447 0.5276 -0.6366 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.8889 7.313e-17 13.02 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.006214 0.9669 -0.04169 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.2063 0.1641 -1.415 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.8874 9.838e-17 12.91 48 1 pearson

NULL

Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.007098 0.9622 -0.04761 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.003244 0.9827 -0.02176 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.003229 0.9828 -0.02166 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.003324 0.9823 -0.0223 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.006214 0.9669 0.04169 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.1118 0.4542 0.755 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.0009188 0.9951 -0.006164 48 1 pearson

NULL

Treat.Tissue

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.2076 0.1614 -1.424 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.8945 2.429e-17 -13.42 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.2368 0.1091 -1.635 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.2367 0.1091 -1.635 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.7671 3.212e-10 -8.021 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.2074 0.1618 -1.422 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.0009188 0.9951 0.006164 48 1 pearson

NULL

Treat.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.2073 0.1621 -1.422 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.003244 0.9827 -0.02176 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.09447 0.5276 -0.6366 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.7536 9.78e-10 7.69 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.09432 0.5283 -0.6355 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.1942 0.1909 -1.328 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.7751 1.599e-10 8.23 48 1 pearson

NULL

Tissue.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.007098 0.9622 -0.04761 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.893 3.267e-17 -13.31 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.8905 5.369e-17 -13.13 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.8874 9.73e-17 -12.91 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.8925 3.661e-17 -13.27 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.889 7.137e-17 -13.03 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.8874 9.838e-17 -12.91 48 1 pearson

NULL

Treat.Tissue.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.2077 0.1613 -1.424 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.893 3.267e-17 -13.31 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.2368 0.1091 -1.635 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.003324 0.9823 -0.0223 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.7873 5.261e-11 -8.565 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.2063 0.1641 -1.415 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.2368 0.1091 -1.635 48 1 pearson

NULL

darkslateblue

Tissue

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.7916 3.487e-11 -8.69 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.7938 2.822e-11 -8.755 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.7926 3.165e-11 -8.72 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.7853 6.349e-11 -8.508 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.7935 2.908e-11 -8.746 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.1597 0.2836 -1.085 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.7853 6.348e-11 -8.508 48 1 pearson

NULL

Treatment

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.1211 0.4175 -0.8183 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.07399 0.6211 -0.4977 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.07409 0.6207 -0.4984 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.7853 6.349e-11 8.508 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.05747 0.7012 -0.3861 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.1199 0.4219 -0.8105 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.7806 9.818e-11 8.377 48 1 pearson

NULL

Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.08218 0.5829 0.5532 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.05036 0.7368 0.3382 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.05022 0.7375 0.3373 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.05126 0.7322 0.3443 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.05747 0.7012 0.3861 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.1597 0.2836 1.085 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.05327 0.7221 0.3579 48 1 pearson

NULL

Treat.Tissue

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.1211 0.4175 -0.8183 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.7938 2.822e-11 -8.755 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.2009 0.1758 -1.375 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.2006 0.1764 -1.374 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.7075 2.696e-08 -6.715 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.1215 0.4158 -0.8214 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.05327 0.7221 -0.3579 48 1 pearson

NULL

Treat.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.1123 0.4523 -0.7582 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.05036 0.7368 0.3382 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.07409 0.6207 -0.4984 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.6943 6.215e-08 6.472 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.06863 0.6467 -0.4615 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.1035 0.4888 -0.698 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.7111 2.125e-08 6.785 48 1 pearson

NULL

Tissue.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.08218 0.5829 0.5532 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.7892 4.384e-11 -8.621 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.7926 3.165e-11 -8.72 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.7806 9.778e-11 -8.378 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.7885 4.689e-11 -8.6 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.787 5.382e-11 -8.558 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.7806 9.818e-11 -8.377 48 1 pearson

NULL

Treat.Tissue.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.1203 0.4207 -0.8127 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.7892 4.384e-11 -8.621 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.2009 0.1758 -1.375 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.05126 0.7322 0.3443 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.7233 9.276e-09 -7.028 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.1199 0.4219 -0.8105 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.2001 0.1775 -1.37 48 1 pearson

NULL

chocolate3

Tissue

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.9136 3.314e-19 15.08 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.9137 3.223e-19 15.09 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.9137 3.266e-19 15.08 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.9113 5.876e-19 14.85 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.9138 3.21e-19 15.09 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.1089 0.4661 0.7351 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.9113 5.878e-19 14.85 48 1 pearson

NULL

Treatment

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.03856 0.7969 0.2589 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.01568 0.9167 0.1052 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.01568 0.9167 0.1052 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.9113 5.876e-19 -14.85 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.009717 0.9483 -0.06519 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.03834 0.798 0.2574 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.9103 7.571e-19 -14.75 48 1 pearson

NULL

Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.02787 0.8525 0.187 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.01133 0.9397 0.07603 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.01133 0.9397 0.07602 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.01148 0.9389 0.07705 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.009717 0.9483 0.06519 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.1089 0.4661 -0.7351 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.009857 0.9476 0.06612 48 1 pearson

NULL

Treat.Tissue

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.03856 0.7969 0.2589 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.9137 3.223e-19 15.09 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.1627 0.2745 1.106 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.1627 0.2745 1.106 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.7753 1.581e-10 8.233 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.03943 0.7924 0.2647 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.009857 0.9476 -0.06612 48 1 pearson

NULL

Treat.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.04114 0.7836 0.2762 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.01133 0.9397 0.07603 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.01568 0.9167 0.1052 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.7683 2.898e-10 -8.052 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.01673 0.9112 0.1122 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.02734 0.8553 0.1834 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.7903 3.946e-11 -8.653 48 1 pearson

NULL

Tissue.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.02787 0.8525 0.187 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.9127 4.148e-19 14.99 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.9137 3.266e-19 15.08 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.9103 7.55e-19 14.75 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.9127 4.22e-19 14.98 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.9126 4.265e-19 14.97 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.9103 7.571e-19 14.75 48 1 pearson

NULL

Treat.Tissue.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.03884 0.7955 0.2607 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.9127 4.148e-19 14.99 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.1627 0.2745 1.106 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.01148 0.9389 0.07705 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.7965 2.153e-11 8.837 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.03834 0.798 0.2574 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.1628 0.2742 1.107 48 1 pearson

NULL

royalblue

Tissue

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.01326 0.9295 0.08895 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.02411 0.8722 0.1618 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.01394 0.9259 0.09355 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.2595 0.07819 1.802 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.02211 0.8827 0.1484 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.3086 0.0348 -2.177 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.2566 0.08171 1.781 48 1 pearson

NULL

Treatment

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.8353 2.852e-13 -10.19 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
-0.8352 2.879e-13 -10.19 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.8785 4.917e-16 -12.33 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.2595 0.07819 -1.802 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.6528 6.61e-07 -5.78 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.8357 2.727e-13 -10.21 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.2904 0.04766 -2.036 48 1 pearson

NULL

Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.3099 0.03403 2.186 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.5635 3.723e-05 4.576 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.3099 0.03405 2.186 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.5444 7.641e-05 4.353 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.6528 6.61e-07 5.78 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.3086 0.0348 2.177 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.5543 5.298e-05 4.467 48 1 pearson

NULL

Treat.Tissue

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.8353 2.852e-13 -10.19 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.02411 0.8722 0.1618 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.8647 4.706e-15 -11.55 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
-0.8222 1.384e-12 -9.69 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.3208 0.02792 -2.272 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.8387 1.853e-13 -10.33 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.5543 5.298e-05 -4.467 48 1 pearson

NULL

Treat.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.8003 1.468e-11 -8.955 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.5635 3.723e-05 4.576 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.8785 4.917e-16 -12.33 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.06652 0.6568 0.4472 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.8003 1.479e-11 -8.953 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.8009 1.388e-11 -8.972 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.04618 0.7579 0.3101 48 1 pearson

NULL

Tissue.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
0.3099 0.03403 2.186 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.05851 0.6961 0.3932 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
0.01394 0.9259 0.09355 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.2927 0.04588 2.053 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
0.06177 0.68 0.4152 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
0.03217 0.83 0.2159 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
0.2904 0.04766 2.036 48 1 pearson

NULL

Treat.Tissue.Time

Partial Correlation Tissue

estimate p.value statistic n gp Method
-0.8322 4.213e-13 -10.07 48 1 pearson

NULL

Partial Correlation Treatment

estimate p.value statistic n gp Method
0.05851 0.6961 0.3932 48 1 pearson

NULL

Partial Correlation Time

estimate p.value statistic n gp Method
-0.8647 4.706e-15 -11.55 48 1 pearson

NULL

Partial Correlation Treat.Tissue

estimate p.value statistic n gp Method
0.5444 7.641e-05 4.353 48 1 pearson

NULL

Partial Correlation Treat.Time

estimate p.value statistic n gp Method
-0.2945 0.0445 -2.067 48 1 pearson

NULL

Partial Correlation Tissue.Time

estimate p.value statistic n gp Method
-0.8357 2.727e-13 -10.21 48 1 pearson

NULL

Partial Correlation Treat.Tissue.Time

estimate p.value statistic n gp Method
-0.8191 1.971e-12 -9.578 48 1 pearson

NULL

Scatterplots Module membership vs. Gene significance

Tissue

tissue.contribution(phenotype, log.tdata.FPKM.subset, MEs)

grey

royalblue

burlywood

orangered1

magenta4

aliceblue

cyan

lavenderblush1

wheat3

green3

paleturquoise4

thistle3

lightblue2

plum

lavenderblush2

magenta1

honeydew

green4

antiquewhite

coral3

indianred3

brown3

dodgerblue4

mediumorchid3

lavenderblush3

mediumpurple

darkslateblue

lightcoral

brown1

pink2

magenta3

deeppink2

chocolate3

orangered4

orange3

blanchedalmond

darkseagreen

darkgrey

lightblue1

darkolivegreen4

firebrick4

Treatment

treat.contribution(phenotype, log.tdata.FPKM.subset, MEs)

grey

royalblue

burlywood

orangered1

magenta4

aliceblue

cyan

lavenderblush1

wheat3

green3

paleturquoise4

thistle3

lightblue2

plum

lavenderblush2

magenta1

honeydew

green4

antiquewhite

coral3

indianred3

brown3

dodgerblue4

mediumorchid3

lavenderblush3

mediumpurple

darkslateblue

lightcoral

brown1

pink2

magenta3

deeppink2

chocolate3

orangered4

orange3

blanchedalmond

darkseagreen

darkgrey

lightblue1

darkolivegreen4

firebrick4

Time

time.contribution(phenotype, log.tdata.FPKM.subset, MEs)

grey

royalblue

burlywood

orangered1

magenta4

aliceblue

cyan

lavenderblush1

wheat3

green3

paleturquoise4

thistle3

lightblue2

plum

lavenderblush2

magenta1

honeydew

green4

antiquewhite

coral3

indianred3

brown3

dodgerblue4

mediumorchid3

lavenderblush3

mediumpurple

darkslateblue

lightcoral

brown1

pink2

magenta3

deeppink2

chocolate3

orangered4

orange3

blanchedalmond

darkseagreen

darkgrey

lightblue1

darkolivegreen4

firebrick4

Treatment by Time

treat.time.contribution(phenotype, log.tdata.FPKM.subset, MEs)

grey

royalblue

burlywood

orangered1

magenta4

aliceblue

cyan

lavenderblush1

wheat3

green3

paleturquoise4

thistle3

lightblue2

plum

lavenderblush2

magenta1

honeydew

green4

antiquewhite

coral3

indianred3

brown3

dodgerblue4

mediumorchid3

lavenderblush3

mediumpurple

darkslateblue

lightcoral

brown1

pink2

magenta3

deeppink2

chocolate3

orangered4

orange3

blanchedalmond

darkseagreen

darkgrey

lightblue1

darkolivegreen4

firebrick4

Treatment by Tissue

treat.tissue.contribution(phenotype, log.tdata.FPKM.subset, MEs)

grey

royalblue

burlywood

orangered1

magenta4

aliceblue

cyan

lavenderblush1

wheat3

green3

paleturquoise4

thistle3

lightblue2

plum

lavenderblush2

magenta1

honeydew

green4

antiquewhite

coral3

indianred3

brown3

dodgerblue4

mediumorchid3

lavenderblush3

mediumpurple

darkslateblue

lightcoral

brown1

pink2

magenta3

deeppink2

chocolate3

orangered4

orange3

blanchedalmond

darkseagreen

darkgrey

lightblue1

darkolivegreen4

firebrick4

Time by Tissue

tissue.time.contribution(phenotype, log.tdata.FPKM.subset, MEs)

grey

royalblue

burlywood

orangered1

magenta4

aliceblue

cyan

lavenderblush1

wheat3

green3

paleturquoise4

thistle3

lightblue2

plum

lavenderblush2

magenta1

honeydew

green4

antiquewhite

coral3

indianred3

brown3

dodgerblue4

mediumorchid3

lavenderblush3

mediumpurple

darkslateblue

lightcoral

brown1

pink2

magenta3

deeppink2

chocolate3

orangered4

orange3

blanchedalmond

darkseagreen

darkgrey

lightblue1

darkolivegreen4

firebrick4

Treatment by Time by Tissue

time.treat.tissue.contribution(phenotype, log.tdata.FPKM.subset, MEs)

grey

royalblue

burlywood

orangered1

magenta4

aliceblue

cyan

lavenderblush1

wheat3

green3

paleturquoise4

thistle3

lightblue2

plum

lavenderblush2

magenta1

honeydew

green4

antiquewhite

coral3

indianred3

brown3

dodgerblue4

mediumorchid3

lavenderblush3

mediumpurple

darkslateblue

lightcoral

brown1

pink2

magenta3

deeppink2

chocolate3

orangered4

orange3

blanchedalmond

darkseagreen

darkgrey

lightblue1

darkolivegreen4

firebrick4

Analysis performed by Ann Wells

The Carter Lab The Jackson Laboratory 2023

ann.wells@jax.org