Reference

Directory initialization

initialize_dir()

Set output directories

Format initialization

initialize_format()

Set format for font and color of plots

Data initialization

reads datasets from the download data files

Exported function

initialize_data()

A wrapper function reads datasets from the download data files

initialize_cnv_data()

Read all CNV related datasets from TCGA

initialize_RNAseq_data()

Read all RNA-seq related datasets from TCGA and GTEx

initialize_survival_data()

Read RNA-seq and survival datasets from TCGA

initialize_proteomics_data()

Read all proteomics related datasets from CCLE and CPTAC LUAD

initialize_phosphoproteomics_data()

Read all phosphoproteomics related datasets from CPTAC LUAD

.get_TCGA_CNV()

Read CNV threshold dataset from TCGA

.get_TCGA_CNV_value()

Read CNV value dataset from TCGA

.get_TCGA_CNV_ratio()

Read CNV ratio dataset from TCGA

.get_TCGA_GTEX_RNAseq()

Read recomputed RNAseq data from both TCGA and GTEx

.get_TCGA_RNAseq()

Read the RNAseq data from TCGA

CNV analysis

CNV analyses of EIF genes in TCGA data

Exported function

EIF4F_CNV_analysis()

Perform all CNV related analysis and generate plots

Internal composite functions to call CNV data analysis and plotting

.plot_bargraph_CNV_TCGA()

Summary of CNV statuses in bar plots

.plot_matrix_CNVcorr_TCGA()

Correlation matrix for CNV values

.plot_boxgraph_CNVratio_TCGA()

CNV ratios in tumors vs adjacent normal tissues across tumor types

Internal functions for CNV data analysis

.CNV_all_cancer()

Calculates the frequency of CNV status in all TCGA cancer types combined

.CNV_ind_cancer()

Calculates the frequency of CNV status in individual TCGA cancer types

.CNVratio_tumor()

Calculates the frequency of CNV status in all TCGA cancer types combined

Internal functions for plotting

.CNV_sum_barplot()

Stacked bar plots of the CNV status summary

.CNV_barplot()

Stacked bar plots of the CNV status

.matrix_plot()

Correlation matrix for gene pairs

.CNVratio_boxplot()

Box plots of the CNV ratios in tumors vs adjacent normals

DEG analysis

Differential gene expression (ratio) analysis of EIF4F genes in TCGA

Exported function

EIF4F_DEG_analysis()

Perform differential gene expression or ratio analysis and generate plots

Internal composite functions to call DEG gene analysis and plotting

.plot_boxgraph_RNAseq_TCGA()

Compare the expression of EIF4F genes

.plot_boxgraph_RNAratio_TCGA()

Compare the RNA ratios between EIF4F genes

Internal functions for differential expression analysis

.RNAseq_all_gene()

Compares expressions among genes in tumor samples

.RNAseq_ind_gene()

Analyzes differential gene expression in tumors vs adjacent normal tissues

.RNAseq_tumortype()

Select gene expression data in primary, metastatic tumors vs adjacent normal tissues from all TCGA cancer types combined

.RNAratio_calculation()

Calculate RNA ratios

.RNAratio_selection()

Select RNA ratio data for plotting

.RNAratio_tumortype()

Analyzes differential RNA ratios in primary, metastatic tumors vs adjacent normal tissues from all TCGA cancer types combined

Internal functions for differential expression analysis plotting

.RNAseq_grouped_boxplot()

Grouped box plots of RNA expression across tumors

.RNAseq_boxplot()

Box plots of differential gene expression across tumors

.violinplot()

Violin plots of differential gene expression/ratio in primary, metastatic tumors vs adjacent normal tissues

.RNAratio_boxplot()

Box plots of differential RNA ratios across tumors

Survival analysis

Survival analyses on EIF4F gene expression in TCGA tumors

Exported function

EIF4F_Survival_analysis()

Perform all related survival analysis and generate plots

Internal composite functions to call survival analysis and plotting

.plot_KM_RNAseq_TCGA()

Survival analyses of TCGA patients with expression in their tumors by Kaplan Meier method

.plot_CoxPH_RNAseq_TCGA()

Survival analyses of TCGA patients with expression in their tumors by Cox-PH method

Internal functions for survival analysis

.KM_curve()

Kaplan Meier survival analyses of gene expression

.univariable_analysis()

Univariable Cox-PH analyses of gene expression

.multivariable_analysis()

Multivariable Cox-PH analyses of gene expression

Internal functions for survival analysis plotting

.forest_graph()

Forest plots of COX-PH results

PCA analysis

PCA on EIF4F expression in GTEx, or/and TCGA studies

Exported function

EIF4F_PCA()

Perform PCA and generate plots

Internal composite functions to call call PCA and plot results

.plot_PCA_TCGA_GTEX()

Perform PCA on RNAseq data from all tumors and healthy tissues

.plot_PCA_TCGA_GTEX_tumor()

Perform PCA on RNAseq data from one tumor type and its matched healthy tissue

.plot_PCA_CPTAC_LUAD()

Perform PCA on proteomics data from CPATC LUADs and matched healthy lung tissues

Internal functions to select RNA-seq data from specific study groups for PCA

.get_df_subset()

Select RNAseq data based on the sample types

Internal functions to perform PCA or imputed PCA

.RNAseq_PCA()

Perform PCA on RNAseq data

.protein_imputePCA()

Perform imputPCA on proteomics data

.biplot_title()

Generate title for PCA plots

Internal functions to plot the PCA results

.biplot()

Plot PCA results as biplot, scree and matrix plots

.selected_biplot()

Plot subgroups of PCA results as biplots

COR analysis

Analyses on EIF4F correlating genes (CORs)

Exported function

EIF4F_Corrgene_analysis()

Perform differential correlation analyses and generate plots

Internal composite functions to analyze the EIF4F CORs

.plot_Corr_RNAseq_TCGA_GTEX()

Perform correlation analysis on RNAseq data from all tumors and healthy tissues

Internal functions to identify correlating genes for EIF4F genes

.EIF_correlation()

Identify EIF4F correlating genes

.correlation_coefficient()

Calculate the correlation co-efficiency between two gene expressions

.is_significant_poscor()

Select positive correlating genes based on coefficiency and pvalue

.is_significant_negcor()

Select negative correlating genes based on coefficiency and pvalue

.summarize_counts()

Summary of total number of CORs identified for each EIF4F gene

Internal functions for correlation analysis and plotting

.CORs_vennplot()

Plot Venn diagrams for correlating genes

.combine_CORs_summary()

Combine the summary of number of posCORs or negCORs from sample types

.CORs_summary_bargraph()

Plot bargraph for the numbers of correlating genes

.combine_CORs_list()

Combine all the EIF4F correlating gene data from tumor and healthy tissues

.is_significant_correlation()

Select both positive and negative correlating genes based on coefficiency and pvalue

.CORs_coeff_heatmap()

Visualize associations between different sources of correlation data and reveal potential pattern

.get_cluster_genes()

Retrieve the gene names from each cluster in heatmap

.pathway_dotplot()

Plot the enriched pathways from gene lists

RNA protein Correlation analysis

Correlation between RNA and protein levels for EIF4F

Exported function

EIF4F_RNA_pro_correlation()

Perform RNA protein correlation and generate scatter plots

Internal composite function to perform RNA protein correlation

.plot_scatter_RNApro_CCLE()

Correlation between CCLE RNAseq and proteomics data

.plot_scatter_RNApro_LUAD()

Correlation between LUAD RNAseq and proteomics data

Internal functions to select EIF RNA/pro data

.get_CCLE_RNAseq_subset()

Select subset of CCLE RNAseq data

.get_CCLE_Proteomics_subset()

Select subset of CCLE proteomics data

Internal functions to plot RNA protein correlation

.RNApro_scatterplot()

Scatter plots of correlation between RNAseq and proteomics data

Phoproteomics and phosphoproteomics analysis

Co-expression and differential expression analysis of EIF4F subunits

Exported function

EIF4F_Proteomics_analysis()

Analyze co-expression among EIF4F subunits and differential expression

Internal composite function for coexpression and differential expression analysis

.plot_scatterplot_protein_CPTAC()

protein-protein coexpression in CPTAC LUAD

.plot_boxgraph_protein_CPTAC()

Comparison of protein and phosphorylation levels among different stages of LUAD

Internal function to select RNA and protein expression data and plotting

.protein_scatterplot()

Scatter plots of protein coexpression

.get_CPTAC_LUAD_Proteomics_subset()

Select subset of CPTAC proteomics data

.get_CPTAC_LUAD_Phosproteomics_subset()

Select subset of CPTAC phosproteomics data

.protein_boxplot()

Boxplots of phosphor-proteomics data across clinic stages