HL60 & MOLM14 impact of IDHmutations and inhibition, RNAseq analysis
Alexis Hucteau
2022-02-28
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Analysis of HL60 MOLM14 IDHm cell lines +/- IDHi
PCA analysis
plot.PCA(PCA_analysis)## Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
fviz_eig(PCA_analysis, addlabels = T)
Variability of gene expression
ggplot(Variability_in_cell_lines, aes(x= Pheno, y = Variability, fill = Pheno))+
geom_boxplot()+
geom_point(size = 0.5)+
xlab("Phenotypes")+
geom_signif(comparisons = list(c("HL60.Mut.AGI5198", "HL60.Mut.DMF"), c("MOLM14.Mut.AGI5198", "MOLM14.Mut.DMF")))+
labs(title = "Gene expression variability depending OS")
TF analysis
HL60_Mut_IDHi_vs_no_treat
plot(HL60_Mut_IDHi_vs_no_treat$mrs)
HL60_Mut_vs_HL60_WT
plot(HL60_Mut_vs_HL60_WT$mrs)
MOLM14_Mut_IDHi_vs_no_treat
plot(MOLM14_Mut_IDHi_vs_no_treat$mrs)
Eigen centrality analysis
HL60 +/- IDHi
Do_cool_scatterplot(HL60_Mut_IDHi_vs_no_treat_network$features, "HL60 +/- IDHi")## Warning: Ignoring unknown parameters: outlier.size
HL60 +/- IDHm
Do_cool_scatterplot(HL60_Mut_vs_HL60_WT_network$features, "HL60 +/- IDHm")## Warning: Ignoring unknown parameters: outlier.size
MOLM14 +/- IDHi
Do_cool_scatterplot(MOLM14_Mut_IDHi_vs_no_treat_network$features, "MOLM14 +/- IDHi")## Warning: Ignoring unknown parameters: outlier.size
RELA and MYC expression in cell lines
RELA in HL60 +/- IDHi Expression
Make_gene_expr_boxplots(Transcriptomes, ID_RELA, "RELA", "HL60.Mut.AGI5198", "HL60_IDHi", "HL60.Mut.DMF", "HL60_DMF", Phenotype)
MYC in HL60 +/- IDHi Expression
Make_gene_expr_boxplots(Transcriptomes, ID_MYC, "MYC", "HL60.Mut.AGI5198", "HL60_IDHi", "HL60.Mut.DMF", "HL60_DMF", Phenotype)
RELA in HL60 +/- IDHm Expression
Make_gene_expr_boxplots(Transcriptomes, ID_RELA, "RELA", "HL60.Mut.None", "HL60_Mut", "HL60.WT.None", "HL60_WT", Phenotype)
MYC in HL60 +/- IDHm Expression
Make_gene_expr_boxplots(Transcriptomes, ID_MYC, "MYC", "HL60.Mut.None", "HL60_Mut", "HL60.WT.None", "HL60_WT", Phenotype)
RELA in MOLM14 +/- IDHi Expression
Make_gene_expr_boxplots(Transcriptomes, ID_RELA, "RELA", "MOLM14.Mut.AGI5198", "MOLM14_IDHi", "MOLM14.Mut.DMF", "MOLM14_DMF", Phenotype)
MYC in MOLM14 +/- IDHi Expression
Make_gene_expr_boxplots(Transcriptomes, ID_MYC, "MYC", "MOLM14.Mut.AGI5198", "MOLM14_IDHi", "MOLM14.Mut.DMF", "MOLM14_DMF", Phenotype)
Network signatures
HL60 IDHm + IDHi vs HL60 IDHm + DMF
HL60 IDHi
HL60 IDHm vs HL60 IDHwt
HL60 m/wt
MOLM14 IDHm + IDHi vs MOLM14 IDHm + DMF
MOLM14 IDHi
Is HL60 a Bad responder and M14 a good responder to IDHi?
TF analysis
HL60 IDHm vs MOLM14 +DOX (IDHm)
plot(HL60_m_vs_M14_m$mrs)
HL60 IDHm + AGI vs MOLM14 +DOX (IDHm) +AGI
plot(HL60_m_agi_vs_M14_m_agi$mrs)
Eigen centrality analysis
HL60 IDHm vs M14 +Dox (IDHm)
Do_cool_scatterplot(HL60_m_vs_M14_m_network$features, "HL60 vs Molm14")## Warning: Ignoring unknown parameters: outlier.size
HL60 IDHm +AGI vs M14 +Dox +AGI
Do_cool_scatterplot(HL60_m_agi_vs_M14_m_agi_network$features, "HL60 vs M14 + IDHm inhib")## Warning: Ignoring unknown parameters: outlier.size
RELA and MYC expression in cell lines
RELA in HL60 IDHm vs M14 IDHm Expression
Make_gene_expr_boxplots(Transcriptomes, ID_RELA, "RELA", "HL60.Mut.DMF", "HL60_IDHm", "MOLM14.Mut.DMF", "M14_DMF", Phenotype)
MYC in HL60 IDHm vs M14 IDHm Expression
Make_gene_expr_boxplots(Transcriptomes, ID_MYC, "MYC", "HL60.Mut.DMF", "HL60_IDHm", "MOLM14.Mut.DMF", "M14_DMF", Phenotype)
RELA in HL60 IDHm +AGI vs M14 IDHm +AGI Expression
Make_gene_expr_boxplots(Transcriptomes, ID_RELA, "RELA", "HL60.Mut.AGI5198", "HL60_IDHi", "MOLM14.Mut.AGI5198", "M14_IDHi", Phenotype)
MYC in HL60 IDHm +AGI vs M14 IDHm +AGI Expression
Make_gene_expr_boxplots(Transcriptomes, ID_MYC, "MYC", "HL60.Mut.AGI5198", "HL60_IDHi", "MOLM14.Mut.AGI5198", "M14_IDHi", Phenotype)