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Cell lines analysis

Source code

Source code

PCA analysis

Koichi’s dataset

plot.PCA(PCA_rnaseq)

fviz_eig(PCA_rnaseq, addlabels = T)

Verhaak’s dataset

plot.PCA(PCA_Verhaak)

fviz_eig(PCA_Verhaak, addlabels = T)

Variability of gene expression

Koichi’s cohort

ggplot(Variability_in_Patients, aes(x= Pheno, y = Variability, fill = Pheno))+
  geom_boxplot()+
  geom_point(size = 0.5)+
  xlab("Phenotypes")+
  geom_signif(comparisons = list(c("NR.B", "R.B"), c("R.B", "R.REL")))+
  labs(title = "Gene expression variability depending IDHi response")

Verhaak Cohort

ggplot(Variability_in_Patients_Verhaak, aes(x= Pheno, y = Variability, fill = Pheno))+
  geom_boxplot()+
  geom_point(size = 0.5)+
  xlab("Phenotypes")+
  geom_signif(comparisons = list(c("High_OS", "Low_OS")))+
  labs(title = "Gene expression variability depending overall survival")

TF analysis

NR vs R IDHi

plot(R_NR_msviper$mrs)

High OS vs Low OS

plot(High_OS_vs_Low_OS_msviper$mrs)

Eigen centrality analysis

NR vs R

Do_cool_scatterplot(NR_R_network$features, "NR vs R")
## Warning: Ignoring unknown parameters: outlier.size

High OS vs Low OS

Do_cool_scatterplot_Ver(High_OS_vs_Low_OS_network$features, "High OS versus Low OS")
## Warning: Ignoring unknown parameters: outlier.size

RELA and MYC expression Patients samples

RELA in NR vs R Expression

Make_gene_expr_boxplots(RNAseq, "RELA", "NR.B", "Bad responder", "R.B", "Good responder", Factor_R_OR_NR_B)

MYC in NR vs R Expression

Make_gene_expr_boxplots(RNAseq, "MYC", "NR.B", "Bad responder", "R.B", "Good responder", Factor_R_OR_NR_B)

RELA in High OS vs Low OS

Make_gene_expr_boxplots(Verhaak_norm_data_SYMBOL, "RELA", "High_OS", "High_OS", "Low_OS", "Low_OS", OS)

MYC in High OS vs Low OS

Make_gene_expr_boxplots(Verhaak_norm_data_SYMBOL, "MYC", "High_OS", "High_OS", "Low_OS", "Low_OS", OS)

Network signatures

NR vs R

NR vs R

High OS vs Low OS

High OS vs Low OS