Data for Translation Efficiency Covariation (TEC) Network Analyses

All data used in this study are placed in the data/ directory of the current codebase. Below is a description of each file. Most datasets are provided directly, while others were obtained from published works, which are cited but not provided here.

• gene_network_data.h5 - Includes filtered TEC and RNA co-expression matrices. Data is sourced from Liu et al.
• tissue_TEC/ - The following files are placed within this subdirectory in the current code implementation.
  • human_brain_TE_rho.rda - Brain specific TEC matrices
  • human_liver_TE_rho.rda - Liver specific TEC matrices
  • human_lung_TE_rho.rda - Lung specific TEC matrices
• protein_abundance.csv - Aggregated protein abundance data for the 11,088 genes analyzed in the study. Data is obtained from PaxDb. Tissues include adrenal gland, colon, esophagus, heart muscle, liver, lung, pancreas, stomach, testis, brain, kidney, rectum, spleen, and thyroid. 
• rna_tissue_hpa.tsv - Unfiltered RNA expression data obtained from Human Protein Atlas.
• rna_prot_genes.txt - List of genes with at least one measurement in any of the nine tissues of interest in both RNA expression and protein abundance datasets.
• tissue_specificity/ - The following files are placed within this subdirectory in the current code implementation. Tissue specificity was determined following the criteria defined by Human Protein Atlas. 
  
  • protein_brain.csv - Tissue-enriched and tissue-enhanced genes for brain protein abundance
  • protein_liver.csv - Tissue-enriched and tissue-enhanced genes for liver protein abundance
  • protein_lung.csv - Tissue-enriched and tissue-enhanced genes for lung protein abundance
  • rna_brain.csv - Tissue-enriched, group-enriched, and tissue-enhanced genes for brain RNA expression. Obtained from Human Protein Atlas
  • rna_liver.csv - Tissue-enriched, group-enriched, and tissue-enhanced genes for liver RNA expression. Obtained from Human Protein Atlas
  • rna_lung.csv - Tissue-enriched, group-enriched, and tissue-enhanced genes for lung RNA expression. Obtained from Human Protein Atlas

Code used for this study can be found at https://github.com/CenikLab/TEC-Network-Analyses.