Notebook for VAE data with metabolic pathways

VAE_Metabolism

Christina Schmidt

23 May 2022

#load the needed libraries:
library(tidyverse) # used for data manipulation
library(rmarkdown) # used for paged_table function

Samples

Here we use:
1. The results of the VAE output of each SiRCle cluster (VAE-Results) for the different comparisons (young-old, Stage4-Stage1, PBRM1-BAP1).
2. The results of the pathway analysis performing fGSEA on the SiRCle clusters. 3. The metabolic signatures used to perform the GSEA based on Gaude et al are used to select specific metabolic pathways of interest.
4. mSigDB signatures: Biocarta, Hallmark, Reactome, KEGG.

#----------------------------------------------------------
#VAE Data
VAE_Stage <- read.csv("InputData/Input_VAE-Results/mean_Integrated_comparison_Stage IV-Stage I.csv", check.names=FALSE)
VAE_Age <- read.csv("InputData/Input_VAE-Results/mean_Integrated_comparison_old-young.csv", check.names=FALSE)
VAE_Mut <- read.csv("InputData/Input_VAE-Results/mean_Integrated_comparison_PBRM1-BAP1.csv", check.names=FALSE)

#----------------------------------------------------------
#fGSEA results
GSEA_Metab_Stage <-read.delim("InputData/Input_VAE-Results/fGSEA/Stage IV-Stage I_consolidated_metabolic_GSEA.tsv",check.names=FALSE)
GSEA_Path_Stage <-read.delim("InputData/Input_VAE-Results/fGSEA/Stage IV-Stage I_consolidated_pathways_GSEA.tsv",check.names=FALSE)
GSEA_Metab_Age <-read.delim("InputData/Input_VAE-Results/fGSEA/old-young_consolidated_metabolic_GSEA.tsv",check.names=FALSE)
GSEA_Path_Age <-read.delim("InputData/Input_VAE-Results/fGSEA/old-young_consolidated_pathways_GSEA.tsv",check.names=FALSE)
GSEA_Metab_Mut <-read.delim("InputData/Input_VAE-Results/fGSEA/PBRM1-BAP1_consolidated_metabolic_GSEA.tsv",check.names=FALSE)
GSEA_Path_Mut <-read.delim("InputData/Input_VAE-Results/fGSEA/PBRM1-BAP1_consolidated_pathways_GSEA.tsv",check.names=FALSE)

#----------------------------------------------------------
#Metabolic Pathway
Metabolic_Signature <-read.csv("InputData/Input_MetabolicPathways_Gaude/41467_2016_BFncomms13041_MOESM340_ESM.csv")

Correction_Metabolic_Signature <- read.csv("InputData/Input_MetabolicPathways_Gaude/41467_2016_BFncomms13041_MOESM341_ESM.csv")%>% 
    mutate(Unique = case_when(associated_Pathways =="1" ~ 'Unique',
                                  TRUE ~ 'In multiple Pathways'))
Metabolic_Signature <-merge(x=Metabolic_Signature, y=Correction_Metabolic_Signature, by.x ="gene", by.y="external_gene_name", all.x=TRUE)

# Other pathways
library(GSEABase)
gmt_to_csv <- function(gmtfile, fast = T){
  if(fast)
  {
    genesets = GSEABase::getGmt(con = gmtfile)
    genesets = unlist(genesets)
    
    gene_to_term =plyr::ldply(genesets,function(geneset){
      temp <- geneIds(geneset)
      temp2 <- setName(geneset)
      temp3 <- as.data.frame(cbind(temp,rep(temp2,length(temp))))
      
    },.progress = plyr::progress_text())
    names(gene_to_term) <- c("gene","term")
    return(gene_to_term[complete.cases(gene_to_term),])
  }
  else
  {
    genesets = getGmt(con = gmtfile)
    genesets = unlist(genesets)
    
    gene_to_term <- data.frame(NA,NA)
    names(gene_to_term) <- c("gene","term")
    for (geneset in genesets)
    {
      temp <- geneIds(geneset)
      temp2 <- setName(geneset)
      temp3 <- as.data.frame(cbind(temp,rep(temp2,length(temp))))
      names(temp3) <- c("gene","term")
      gene_to_term <- rbind(gene_to_term,temp3)
    }
    
    return(gene_to_term[complete.cases(gene_to_term),])
  }
}#Load the Pathways

KEGG <- gmt_to_csv("InputData/Input_MSigDB_Signatures/c2.cp.kegg.v6.2.symbols.gmt")

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Reactome <- gmt_to_csv("InputData/Input_MSigDB_Signatures/c2.cp.reactome.v6.2.symbols.gmt")

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Biocarta <- gmt_to_csv("InputData/Input_MSigDB_Signatures/c2.cp.biocarta.v6.2.symbols.gmt")

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Hallmarks <- gmt_to_csv("InputData/Input_MSigDB_Signatures/h.all.v6.2.symbols.gmt")

## 
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Pathways <- rbind(KEGG, Reactome, Biocarta, Hallmarks)

Plots VAE Mean Integrated Rank

This refers to the results of the VAE built for the individual SiRCle clusters.

Lollipop Graphs

#Prepare the DF needed:
InputLollipop <- function(Input, Condition1, Condition2){
  Cond1 <-Input[,-9]
  names(Cond1)[8]<-"Integrated Mean"
  Cond1$Condition <- paste(Condition1)
  
  Cond2 <-Input[,-8]
  names(Cond2)[8]<-"Integrated Mean"
  Cond2$Condition <- paste(Condition2)

  Graph <- rbind(Cond1,Cond2)
  Graph$`Integrated value_Round` <- round(Graph$`Integrated Mean`, digits = 2)
  Graph$Colour <- ifelse(Graph$Condition== paste(Condition1) , 3, 14)
  Output <- Graph
}

Graph_Stage<-InputLollipop(Input= VAE_Stage, 
                           Condition1="Stage 1", 
                           Condition2="Stage 4")

Graph_Age<-InputLollipop(Input= VAE_Age, 
                           Condition1="Young", 
                           Condition2="Old")

Graph_Mut<-InputLollipop(Input= VAE_Mut, 
                           Condition1="BAP1", 
                           Condition2="PBRM1")

#-----------------------------------------------
Lollipop_VAE <- function(Input, Signature, Signature_term, Comparison){
  SiRCle_Clusters <- c("MDE", "MDS", "TPDE", "TPDS", "TMDE", "TMDS", "MDS_TMDE","MDE_TMDS","TPDE_TMDS", "TPDS_TMDE")
    for (k in SiRCle_Clusters){
  Input_Cluster <- subset(Input, Regulation_Grouping_2 == paste(k))
      Pathway <- subset(Signature, term == paste(Signature_term))
      Plot  <- merge(x=Pathway,y=Input_Cluster, by.x="gene", by.y="external_gene_name", all.x=TRUE)
      Plot  <- na.omit(Plot)
  #Plot
   if(nrow(Plot)>1){    
  Dotplot1 <-ggplot(Plot, aes(x=reorder(gene, + `Integrated Mean`), y=`Integrated Mean`, label=`Integrated value_Round`)) + 
    geom_point(stat='identity', aes(size = `Integrated Mean`, col=Condition))  +
    geom_segment(aes(y =(Reduce(max,`Integrated Mean`)), 
                   x = gene, 
                   yend = `Integrated Mean`,
                   xend = gene), 
               color = "black") +
    scale_size(name="VAE Integrated Rank (Mean)",range = c(2,16))+
    geom_text(color="black", size=2) +
    labs(title=paste(Signature_term), 
        subtitle=paste(k)) + 
    ylim(((Reduce(min,Plot$`Integrated Mean`))-0.5),((Reduce(max,Plot$`Integrated Mean`))+0.5)) +
    theme_minimal() +
    coord_flip()+
    theme(plot.title = element_text(color = "black", size = 12, face = "bold"),
          plot.subtitle = element_text(color = "black", size=10),
          plot.caption = element_text(color = "black",size=9, face = "italic", hjust = 2.5))+
    labs(y="VAE integrated value", x="")
  ggsave(file=paste("Figures/Lollipop_IntegratedMean/", k,"_LollipopGraph_",Signature_term, Comparison,".pdf", sep=""), plot=Dotplot1, width=10, height=10)
  plot(Dotplot1)
   } else{
        print(paste(Signature_term, " pathway genes not present in SiRCle cluster ", k, sep=""))
        }
    }
}

#Run the function:
Pathway_Names <- Metabolic_Signature[!duplicated(Metabolic_Signature$term),]
Pathway_Names <- Pathway_Names$term

##Stage
for (i in Pathway_Names){
  Lollipop_VAE(Input=Graph_Stage,
            Signature= Metabolic_Signature,
            Signature_term=i,
            Comparison="_Stage IV-Stage I")
}

## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Ketone Bodies Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Ketone Bodies Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Ketone Bodies Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster MDE"

## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Xenobiotics Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Xenobiotics Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Xenobiotics Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "GABA shunt pathway genes not present in SiRCle cluster MDE"

## [1] "GABA shunt pathway genes not present in SiRCle cluster TPDE"

## [1] "GABA shunt pathway genes not present in SiRCle cluster TMDE"

## [1] "GABA shunt pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "GABA shunt pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "GABA shunt pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Multidrug resistance pathway genes not present in SiRCle cluster MDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDE"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TMDE"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TMDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycerophospholipid Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Glycerophospholipid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Steroid Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Eicosanoid Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Eicosanoid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Eicosanoid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Urea Cycle pathway genes not present in SiRCle cluster MDE"
## [1] "Urea Cycle pathway genes not present in SiRCle cluster MDS"
## [1] "Urea Cycle pathway genes not present in SiRCle cluster TPDE"

## [1] "Urea Cycle pathway genes not present in SiRCle cluster TMDS"
## [1] "Urea Cycle pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Urea Cycle pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster MDE"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TPDE"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster MDE"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster TPDE"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Valine, Leucine and Isoleucine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Valine, Leucine and Isoleucine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Valine, Leucine and Isoleucine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Citric Acid Cycle pathway genes not present in SiRCle cluster MDE"

## [1] "Citric Acid Cycle pathway genes not present in SiRCle cluster TMDE"

## [1] "Citric Acid Cycle pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Alanine and Aspartate Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Alanine and Aspartate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Alanine and Aspartate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Purine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Purine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Retinol Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Retinol Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "ROS Detoxification pathway genes not present in SiRCle cluster TPDE"

## [1] "ROS Detoxification pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDE"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDS"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TPDE"

## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TMDE"

## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDS"

## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TPDS"

## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDS"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDS"

## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TMDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TMDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Glycine, Serine and Threonine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Glycine, Serine and Threonine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Glycine, Serine and Threonine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Cysteine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Cysteine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Sugar Degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TPDE"

## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Sugar Degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Folate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster MDE"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster MDS"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDE"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDS"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TMDE"

## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Transport, Extracellular pathway genes not present in SiRCle cluster TPDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster MDE"
## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster MDS"
## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster TPDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster TMDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDE"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDS"

## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster TMDE"

## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster TMDS"

## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Galactose metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Galactose metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "NAD Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "NAD Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "NAD Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "NAD Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "NAD Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDE"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDS"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster TPDE"

## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster TMDE"

## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Vitamin D pathway genes not present in SiRCle cluster MDE"
## [1] "Vitamin D pathway genes not present in SiRCle cluster MDS"
## [1] "Vitamin D pathway genes not present in SiRCle cluster TPDE"

## [1] "Vitamin D pathway genes not present in SiRCle cluster TMDE"

## [1] "Vitamin D pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Vitamin D pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Vitamin D pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Vitamin D pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDE"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TPDE"

## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TMDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TPDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TPDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TMDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TMDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Histone Methylation pathway genes not present in SiRCle cluster MDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDE"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TMDE"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TMDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster MDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster MDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDS"

## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TMDS"

## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Protein Modification pathway genes not present in SiRCle cluster MDS"

## [1] "Protein Modification pathway genes not present in SiRCle cluster TPDS"

## [1] "Protein Modification pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Protein Modification pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Protein Modification pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Protein Modification pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TPDE"

## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TMDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TMDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster MDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDE"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TMDE"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TMDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TMDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TMDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDS_TMDE"

##Age
for (i in Pathway_Names){
  Lollipop_VAE(Input=Graph_Age,
            Signature= Metabolic_Signature,
            Signature_term=i,
            Comparison="_old-young")
}

## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Ketone Bodies Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Ketone Bodies Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Ketone Bodies Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster MDE"

## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Xenobiotics Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Xenobiotics Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Xenobiotics Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "GABA shunt pathway genes not present in SiRCle cluster MDE"

## [1] "GABA shunt pathway genes not present in SiRCle cluster TPDE"

## [1] "GABA shunt pathway genes not present in SiRCle cluster TMDE"

## [1] "GABA shunt pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "GABA shunt pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "GABA shunt pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Multidrug resistance pathway genes not present in SiRCle cluster MDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDE"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TMDE"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TMDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycerophospholipid Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Glycerophospholipid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Steroid Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Eicosanoid Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Eicosanoid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Eicosanoid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Urea Cycle pathway genes not present in SiRCle cluster MDE"
## [1] "Urea Cycle pathway genes not present in SiRCle cluster MDS"
## [1] "Urea Cycle pathway genes not present in SiRCle cluster TPDE"

## [1] "Urea Cycle pathway genes not present in SiRCle cluster TMDS"
## [1] "Urea Cycle pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Urea Cycle pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster MDE"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TPDE"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster MDE"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster TPDE"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Valine, Leucine and Isoleucine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Valine, Leucine and Isoleucine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Valine, Leucine and Isoleucine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Citric Acid Cycle pathway genes not present in SiRCle cluster MDE"

## [1] "Citric Acid Cycle pathway genes not present in SiRCle cluster TMDE"

## [1] "Citric Acid Cycle pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Alanine and Aspartate Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Alanine and Aspartate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Alanine and Aspartate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Purine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Purine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Retinol Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Retinol Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "ROS Detoxification pathway genes not present in SiRCle cluster TPDE"

## [1] "ROS Detoxification pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDE"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDS"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TPDE"

## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TMDE"

## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDS"

## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TPDS"

## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDS"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDS"

## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TMDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TMDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Glycine, Serine and Threonine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Glycine, Serine and Threonine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Glycine, Serine and Threonine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Cysteine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Cysteine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Sugar Degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TPDE"

## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Sugar Degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Folate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster MDE"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster MDS"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDE"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDS"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TMDE"

## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Transport, Extracellular pathway genes not present in SiRCle cluster TPDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster MDE"
## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster MDS"
## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster TPDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster TMDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDE"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDS"

## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster TMDE"

## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster TMDS"

## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Galactose metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Galactose metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "NAD Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "NAD Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "NAD Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "NAD Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "NAD Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDE"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDS"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster TPDE"

## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster TMDE"

## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Vitamin D pathway genes not present in SiRCle cluster MDE"
## [1] "Vitamin D pathway genes not present in SiRCle cluster MDS"
## [1] "Vitamin D pathway genes not present in SiRCle cluster TPDE"

## [1] "Vitamin D pathway genes not present in SiRCle cluster TMDE"

## [1] "Vitamin D pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Vitamin D pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Vitamin D pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Vitamin D pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDE"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TPDE"

## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TMDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TPDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TPDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TMDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TMDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Histone Methylation pathway genes not present in SiRCle cluster MDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDE"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TMDE"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TMDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster MDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster MDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDS"

## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TMDS"

## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Protein Modification pathway genes not present in SiRCle cluster MDS"

## [1] "Protein Modification pathway genes not present in SiRCle cluster TPDS"

## [1] "Protein Modification pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Protein Modification pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Protein Modification pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Protein Modification pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TPDE"

## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TMDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TMDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster MDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDE"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TMDE"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TMDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TMDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TMDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDS_TMDE"

##Mutation
for (i in Pathway_Names){
  Lollipop_VAE(Input=Graph_Mut,
            Signature= Metabolic_Signature,
            Signature_term=i,
            Comparison="_PBRM1-BAP1")
}

## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Sphingolipid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "O-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Ketone Bodies Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Ketone Bodies Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Ketone Bodies Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster MDE"

## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acid Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Fatty Acid Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Xenobiotics Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Xenobiotics Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Xenobiotics Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Tryptophan metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Lysine Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "GABA shunt pathway genes not present in SiRCle cluster MDE"

## [1] "GABA shunt pathway genes not present in SiRCle cluster TPDE"

## [1] "GABA shunt pathway genes not present in SiRCle cluster TMDE"

## [1] "GABA shunt pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "GABA shunt pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "GABA shunt pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Cholesterol Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Bile Acid Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Multidrug resistance pathway genes not present in SiRCle cluster MDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDE"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TMDE"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TMDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Multidrug resistance pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycerophospholipid Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Glycerophospholipid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Steroid Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Nucleotide Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Eicosanoid Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Eicosanoid Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Eicosanoid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Blood Group Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Arginine and Proline Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Histidine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Tyrosine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Urea Cycle pathway genes not present in SiRCle cluster MDE"
## [1] "Urea Cycle pathway genes not present in SiRCle cluster MDS"
## [1] "Urea Cycle pathway genes not present in SiRCle cluster TPDE"

## [1] "Urea Cycle pathway genes not present in SiRCle cluster TMDS"
## [1] "Urea Cycle pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Urea Cycle pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Phenylalanine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "beta-Alanine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster MDE"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TPDE"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Fatty Acids Oxidation, peroxisomal pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster MDE"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster TPDE"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster TMDE"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Fatty Acids Oxidation, mitochondrial pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Valine, Leucine and Isoleucine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Valine, Leucine and Isoleucine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Valine, Leucine and Isoleucine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Citric Acid Cycle pathway genes not present in SiRCle cluster MDE"

## [1] "Citric Acid Cycle pathway genes not present in SiRCle cluster TMDE"

## [1] "Citric Acid Cycle pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Riboflavin Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Methionine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Glutamate metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Alanine and Aspartate Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Alanine and Aspartate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Alanine and Aspartate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Purine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Purine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Polyamines Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Cyclic Nucleotides Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Retinol Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Retinol Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Ethanol Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "ROS Detoxification pathway genes not present in SiRCle cluster TPDE"

## [1] "ROS Detoxification pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDE"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDS"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TPDE"

## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TMDE"

## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "DNA Demethylation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glutathione Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDS"

## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TPDS"

## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Purine Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDS"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "N-Glycan Degradation pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Keratan sulfate degradation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDS"

## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TMDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TMDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glycogen Degradation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Triacylglycerol Synthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pyruvate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Glycine, Serine and Threonine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Glycine, Serine and Threonine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Glycine, Serine and Threonine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Selenoamino acid metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Cysteine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Cysteine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Pyrimidine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Sugar Degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TPDE"

## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Sugar Degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Sugar Degradation pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Porphyrin and Heme Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Folate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Folate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "N-Glycan Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Amino and Nucleotide Sugar Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster MDE"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster MDS"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDE"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDS"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TMDE"

## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Transport, Mitochondrial pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Chondroitin sulfate degradation pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Transport, Extracellular pathway genes not present in SiRCle cluster TPDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster MDE"
## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster MDS"
## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster TPDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster TMDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Oxidative Phosphorylation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDE"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDS"

## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster TMDE"

## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Transport, Lysosomal pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster TMDS"

## [1] "Chondroitin and Heparan sulfate biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Keratan sulfate biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Galactose metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Galactose metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Galactose metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Biotin Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Carbonic Acid Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pyrimidine Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "NAD Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "NAD Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "NAD Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "NAD Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "NAD Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Taurine and hypotaurine metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Creatine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "CoA Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Ubiquinone Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDE"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDS"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster TPDE"

## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster TMDE"

## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster MDE_TMDS"

## [1] "Carnitine shuttle pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "CYP Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Vitamin D pathway genes not present in SiRCle cluster MDE"
## [1] "Vitamin D pathway genes not present in SiRCle cluster MDS"
## [1] "Vitamin D pathway genes not present in SiRCle cluster TPDE"

## [1] "Vitamin D pathway genes not present in SiRCle cluster TMDE"

## [1] "Vitamin D pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Vitamin D pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Vitamin D pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Vitamin D pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDE"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TPDE"

## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TMDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pentose Phosphate Pathway pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TPDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TPDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TMDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TMDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "DNA Methylation pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Histone Methylation pathway genes not present in SiRCle cluster MDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDE"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TMDE"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TMDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Histone Methylation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster MDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster MDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TMDE"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TMDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "DNA Synthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Fructose and Mannose Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDE"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDS"

## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TMDS"

## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glycogen Synthesis pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDE"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDS"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TPDE"

## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TMDE"

## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Pterin Biosynthesis pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Protein Modification pathway genes not present in SiRCle cluster MDS"

## [1] "Protein Modification pathway genes not present in SiRCle cluster TPDS"

## [1] "Protein Modification pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Protein Modification pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Protein Modification pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Protein Modification pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster MDE"

## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Glyoxylate and Dicarboxylate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TMDE"

## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Heparan sulfate degradation pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Hyaluronan Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"

## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Propanoate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDS"

## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Inositol Phosphate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"

## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Vitamin B12 Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Vitamin B6 Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TMDE"

## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Phosphate Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster MDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TPDE"

## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TMDE"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TMDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Thiamine Metabolism pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TPDE"

## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TMDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TMDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Ascorbate uptake pathway genes not present in SiRCle cluster TPDS_TMDE"

## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster MDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDE"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TMDE"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TMDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Transport, Golgi Apparatus pathway genes not present in SiRCle cluster TPDS_TMDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TMDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TMDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDS_TMDE"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster MDE_TMDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDE_TMDS"
## [1] "Transport, Endoplasmic Reticular pathway genes not present in SiRCle cluster TPDS_TMDE"

Next we plot all genes of different SiRCle clusters corresponding to the same metabolic pathway on one lollipop graph.

Lollipop_All_VAE_Clusters <- function(Input, Signature, Signature_term, Comparison){
  #Select the pathway
      Pathway <- subset(Signature, term == paste(Signature_term))
      Plot  <- merge(x=Pathway,y=Input, by.x="gene", by.y="external_gene_name", all.x=TRUE)
      Plot  <- na.omit(Plot)
   #Plot
      if(nrow(Plot)>1){    
        Dotplot1 <-ggplot(Plot, aes(x=reorder(gene, + `Integrated Mean`), y=`Integrated Mean`, label=`Integrated value_Round`)) + 
    geom_point(stat='identity', aes(size = `Integrated Mean`, col=Condition))  +
    geom_segment(aes(y =(Reduce(max,`Integrated Mean`)), 
                   x = gene, 
                   yend = `Integrated Mean`,
                   xend = gene), 
               color = "black") +
   scale_size(name="VAE Integrated Rank (Mean)",range = c(2,16))+
    geom_text(color="black", size=2) +
    labs(title=paste(Signature_term), 
        subtitle="All SiRCle Clusters") + 
    ylim(((Reduce(min,Plot$`Integrated Mean`))-0.5),((Reduce(max,Plot$`Integrated Mean`))+0.5)) +
    theme_minimal() +
    coord_flip()+
    theme(axis.text.y = element_text(color = "black", size=9, face = "bold"),
          plot.title = element_text(color = "black", size = 12, face = "bold"),
          plot.subtitle = element_text(color = "black", size=10))+
          #plot.caption = element_text(color = "black",size=9, face = "italic", hjust = 2.5))+
    labs(y="VAE integrated value", x="")
  ggsave(file=paste("Figures/Lollipop_IntegratedMean/AllClusters_LollipopGraph_",Signature_term, Comparison,".pdf", sep=""), plot=Dotplot1, width=10, height=10)
  plot(Dotplot1)
     } else{
       print(paste(Signature_term, " pathway genes not present in any SiRCle cluster ", sep=""))
       }
}

#Run the function:
Pathway_Names <- Metabolic_Signature[!duplicated(Metabolic_Signature$term),]
Pathway_Names <- Pathway_Names$term

for (i in Pathway_Names){
  Lollipop_All_VAE_Clusters(Input=Graph_Stage,
            Signature= Metabolic_Signature,
            Signature_term=i,
            Comparison="_Stage IV-Stage I")
}

## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in any SiRCle cluster "

## [1] "Hyaluronan Metabolism pathway genes not present in any SiRCle cluster "

## [1] "Transport, Endoplasmic Reticular pathway genes not present in any SiRCle cluster "

for (i in Pathway_Names){
  Lollipop_All_VAE_Clusters(Input=Graph_Age,
            Signature= Metabolic_Signature,
            Signature_term=i,
            Comparison="_old-young")
}

## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in any SiRCle cluster "

## [1] "Hyaluronan Metabolism pathway genes not present in any SiRCle cluster "

## [1] "Transport, Endoplasmic Reticular pathway genes not present in any SiRCle cluster "

for (i in Pathway_Names){
  Lollipop_All_VAE_Clusters(Input=Graph_Mut,
            Signature= Metabolic_Signature,
            Signature_term=i,
            Comparison="_PBRM1-BAP1")
}

## [1] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathway genes not present in any SiRCle cluster "

## [1] "Hyaluronan Metabolism pathway genes not present in any SiRCle cluster "

## [1] "Transport, Endoplasmic Reticular pathway genes not present in any SiRCle cluster "

Plots GSE

fGSEA

This is based on the Gene set enrichment analysis (GSEA) results using the metabolic signatures and the pathways from the MSig DB (KEGG, Reactome, Biocarta, Hallmarks) . Here we use the following threshold:

1. Given that the input data are quite small and specific (in the sense of pathways they correspond to). Indeed e.g. in MDE only 32 pathways that have a gene detected in them, which will change the results for multiple testing, hence we use p.val <0.25 as the significant threshold

2. Given the pathway sizes are mostly really small (5 genes in one pathway), at least 10% of a pathway has to be detected.

# Add information on pathway size to the Signatures
SignatureCount <- function(Signature){
  DF<- Signature
  DF$Count <- 1
  DF$Count1 <- 1
  
  DF_Mean <- (DF[,3:4]) %>%
    group_by(DF$term) %>%
    summarise_all(funs(sum))%>%
    rename("DF$term"="term",
           "Count"="Genes_in_Pathway")
  DF_Mean <- DF_Mean[,-3]

  Output <- merge(x= DF[,1:2], y=DF_Mean, by="term", all.x=TRUE)
}


Metabolic_Signature_Count <- SignatureCount(Signature=Metabolic_Signature[,1:2])
Pathway_Count <- SignatureCount(Signature=Pathways)


# Add information on Pathway size to GSEA output and Select the Pathways to plot based on the threshold
Select_Pathway <- function(Input, Pathway_Count, FileName){
  DF <- merge(x= Input, y=Pathway_Count,by.x="Pathway", by.y="term", all.x=TRUE)
  DF$Percentage_of_Pathway_detected <-round(((DF$`fGSEA size`/DF$Genes_in_Pathway)*100),digits=2)
  DF  <- DF  %>%
    mutate(`In Threshold?` = case_when(`fGSEA pval` <= 0.25 &  Percentage_of_Pathway_detected>= 10 & Genes_in_Pathway >=5 ~ 'YES',
                                  `fGSEA pval` > 0.25 |  Percentage_of_Pathway_detected< 10 | Genes_in_Pathway < 5~ 'NO',
                                  TRUE ~ 'FALSE'))
  write.csv(DF,paste("OutputData/",FileName , ".csv"), row.names = FALSE)
  Output<- DF
}


GSEA_Metab_Stage <- Select_Pathway(Input=GSEA_Metab_Stage,
                                Pathway_Count=Metabolic_Signature_Count, 
                                FileName="Stage IV-Stage I_consolidated_metabolic_GSEA")
  
GSEA_Path_Stage <- Select_Pathway(Input=GSEA_Path_Stage,
                                Pathway_Count=Pathway_Count, 
                                FileName="Stage IV-Stage I_consolidated_pathways_GSEA")

GSEA_Metab_Age <-Select_Pathway(Input=GSEA_Metab_Age,
                                Pathway_Count=Metabolic_Signature_Count, 
                                FileName="old-young_consolidated_metabolic_GSEA")

GSEA_Path_Age <-Select_Pathway(Input=GSEA_Path_Age,
                                Pathway_Count=Pathway_Count, 
                                FileName="old-young_consolidated_pathways_GSEA")

GSEA_Metab_Mut <-Select_Pathway(Input=GSEA_Metab_Mut,
                                Pathway_Count=Metabolic_Signature_Count, 
                                FileName="PBRM1-BAP1_consolidated_metabolic_GSEA")

GSEA_Path_Mut <-Select_Pathway(Input=GSEA_Path_Mut,
                                Pathway_Count=Pathway_Count, 
                                FileName="PBRM1-BAP1_consolidated_pathways_GSEA")

#make the function:
Lollipop_fGSEA <- function(Input, fGSEA_Signature ,Comparison){
  #Make colour code
  keyvals<- ifelse(
    Input$Regulation_Grouping_2 == "MDS", "#CF4692",
    ifelse(Input$Regulation_Grouping_2 == "MDS&TMDE", "#A16BAA",
    ifelse(Input$Regulation_Grouping_2 == "MDE", "#6AAF43",
    ifelse(Input$Regulation_Grouping_2 == "MDE&TMDS", "#0E8D6D",
    ifelse(Input$Regulation_Grouping_2 == "TPDS", "#452D76",
    ifelse(Input$Regulation_Grouping_2 == "TPDS&TMDE", "#7E4090",
    ifelse(Input$Regulation_Grouping_2 == "TPDE", "#E58D26",
    ifelse(Input$Regulation_Grouping_2 == "TPDE&TMDS", "#844D13",
    ifelse(Input$Regulation_Grouping_2 == "TMDS", "#3A58A3",
    ifelse(Input$Regulation_Grouping_2 == "TMDE", "#E5322F",
    ifelse(Input$Regulation_Grouping_2 == "None", "grey",       
           "black")))))))))))
  names(keyvals)[is.na(keyvals)] <- "black"
  names(keyvals)[keyvals == 'black'] <- "NA"
  names(keyvals)[keyvals == '#CF4692'] <- "MDS"
  names(keyvals)[keyvals == '#A16BAA'] <- "MDS&TMDE"
  names(keyvals)[keyvals == '#6AAF43'] <- "MDE"
  names(keyvals)[keyvals == '#0E8D6D'] <- "MDE&TMDS"
  names(keyvals)[keyvals == '#452D76'] <- "TPDS"
  names(keyvals)[keyvals == '#7E4090'] <- "TPDS&TMDE"
  names(keyvals)[keyvals == '#E58D26'] <- "TPDE"
  names(keyvals)[keyvals == '#844D13'] <- "TPDE&TMDS"
  names(keyvals)[keyvals == '#3A58A3'] <- "TMDS"
  names(keyvals)[keyvals == '#E5322F'] <- "TMDE"
  names(keyvals)[keyvals == 'grey'] <- "None"
  
  #Select only pathways that meet the threshold
  Input_Select <-Input%>%
    subset(`In Threshold?`=="YES")
  
  if(nrow(Input_Select)>1){   
  #Plot
  Dotplot <-ggplot(Input_Select, aes(x=reorder(Pathway, +Percentage_of_Pathway_detected), y=`fGSEA NES`, label=Percentage_of_Pathway_detected)) + 
    geom_point(stat='identity', aes(size =Percentage_of_Pathway_detected, col=Regulation_Grouping_2)) +
     scale_color_manual(values = keyvals)+
    geom_segment(aes(y = 0, 
                   x = Pathway, 
                   yend = `fGSEA NES`,
                   xend = Pathway), 
               color = "black") +
   scale_size(name="Genes detected of pathway [%]",range = c(2,16))+
    geom_text(color="black", size=2) +
    labs(title= fGSEA_Signature,
        subtitle= Comparison,
        caption="*Threshold: p.val<0.25 & Genes detected of pathway > 10%") + 
    ylim(((Reduce(min,Input_Select$`fGSEA NES`))-0.5),((Reduce(max,Input_Select$`fGSEA NES`))+0.5)) +
    theme_bw() +
    coord_flip()+
    theme(plot.title = element_text(color = "black", size = 12, face = "bold"),
          plot.subtitle = element_text(color = "black", size=10),
          plot.caption = element_text(color = "black",size=9, face = "italic", hjust = 2.5))+
    labs(y="NES", x="")
  ggsave(file=paste("Figures/Lollipop_fGSEA/fGSEA_LollipopGraph",fGSEA_Signature, Comparison,".pdf", sep=""), plot=Dotplot, width=15, height=10)
  
  plot(Dotplot)
  } else{
       print(paste("GSEA of comparing ", Comparison, " patients does not lead to any altered pathways that pass the threshold criteria", sep=""))
       }
}

#Make the Graphs:
Lollipop_fGSEA(Input=GSEA_Metab_Stage,
               fGSEA_Signature= "_Metabolic_" ,
               Comparison="Stage IV-Stage I")

Lollipop_fGSEA(Input=GSEA_Path_Stage,
               fGSEA_Signature= "_Kegg-Reactome-Biocarta-hallmark_" ,
               Comparison="Stage IV-Stage I")

Lollipop_fGSEA(Input=GSEA_Metab_Age,
               fGSEA_Signature= "_Metabolic_" ,
               Comparison="old-young")

Lollipop_fGSEA(Input=GSEA_Path_Age,
               fGSEA_Signature= "_Kegg-Reactome-Biocarta-hallmark_" ,
               Comparison="old-young")

Lollipop_fGSEA(Input=GSEA_Metab_Mut,
               fGSEA_Signature= "_Metabolic_" ,
               Comparison="PBRM1-BAP1")

Lollipop_fGSEA(Input=GSEA_Path_Mut,
               fGSEA_Signature= "_Kegg-Reactome-Biocarta-hallmark_" ,
               Comparison="PBRM1-BAP1")

Information about packages and versions used

sessionInfo()

## R version 4.2.0 (2022-04-22 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 17134)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_United Kingdom.1252 
## [2] LC_CTYPE=English_United Kingdom.1252   
## [3] LC_MONETARY=English_United Kingdom.1252
## [4] LC_NUMERIC=C                           
## [5] LC_TIME=English_United Kingdom.1252    
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] GSEABase_1.58.0      graph_1.74.0         annotate_1.74.0     
##  [4] XML_3.99-0.10        AnnotationDbi_1.58.0 IRanges_2.30.0      
##  [7] S4Vectors_0.34.0     Biobase_2.56.0       BiocGenerics_0.42.0 
## [10] rmarkdown_2.14       forcats_0.5.1        stringr_1.4.0       
## [13] dplyr_1.0.9          purrr_0.3.4          readr_2.1.2         
## [16] tidyr_1.2.0          tibble_3.1.7         ggplot2_3.3.6       
## [19] tidyverse_1.3.1     
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-7           fs_1.5.2               lubridate_1.8.0       
##  [4] bit64_4.0.5            httr_1.4.3             GenomeInfoDb_1.32.2   
##  [7] tools_4.2.0            backports_1.4.1        bslib_0.3.1           
## [10] utf8_1.2.2             R6_2.5.1               DBI_1.1.3             
## [13] colorspace_2.0-3       withr_2.5.0            tidyselect_1.1.2      
## [16] bit_4.0.4              compiler_4.2.0         cli_3.3.0             
## [19] rvest_1.0.2            xml2_1.3.3             labeling_0.4.2        
## [22] sass_0.4.1             scales_1.2.0           digest_0.6.29         
## [25] XVector_0.36.0         pkgconfig_2.0.3        htmltools_0.5.2       
## [28] highr_0.9              dbplyr_2.2.0           fastmap_1.1.0         
## [31] rlang_1.0.2            readxl_1.4.0           rstudioapi_0.13       
## [34] RSQLite_2.2.14         farver_2.1.0           jquerylib_0.1.4       
## [37] generics_0.1.2         jsonlite_1.8.0         RCurl_1.98-1.7        
## [40] magrittr_2.0.3         GenomeInfoDbData_1.2.8 Rcpp_1.0.8.3          
## [43] munsell_0.5.0          fansi_1.0.3            lifecycle_1.0.1       
## [46] stringi_1.7.6          yaml_2.3.5             zlibbioc_1.42.0       
## [49] plyr_1.8.7             grid_4.2.0             blob_1.2.3            
## [52] crayon_1.5.1           Biostrings_2.64.0      haven_2.5.0           
## [55] hms_1.1.1              KEGGREST_1.36.2        knitr_1.39            
## [58] pillar_1.7.0           reprex_2.0.1           glue_1.6.2            
## [61] evaluate_0.15          modelr_0.1.8           png_0.1-7             
## [64] vctrs_0.4.1            tzdb_0.3.0             cellranger_1.1.0      
## [67] gtable_0.3.0           assertthat_0.2.1       cachem_1.0.6          
## [70] xfun_0.31              xtable_1.8-4           broom_0.8.0           
## [73] memoise_2.0.1          ellipsis_0.3.2