Translation Efficiency Covariation (TEC) Network Analyses

This repository contains code supporting the manuscript titled Topological and Functional Characterization of Human Translation Efficiency Covariation Network. It includes scripts used for:

• Characterization of the TEC network
• Comparative analysis with the corresponding RNA co-expression network
• Functional analysis of the TEC network
• Analysis of tissue-specific TEC networks
• Supplementary and supporting analyses

Overview

The following Jupyter notebooks correspond to the four results subsections of the manuscript:

1. tec_characterization.ipynb - Characterization of TEC network
2. rna_comparison.ipynb - Comparison between the TEC network and the RNA co-expression network; includes Supplementary Figure 2a and Table 3
3. tec_biology.ipynb - Functional analysis and clustering of the TEC network
4. tissue_net.ipynb - Analysis of the liver-specific TEC network
5. supplemental/ - All supplemental analyses, figures, and tables generation

Workflow

To run any of the analyses, open the corresponding .ipynb file and select Run All.

If you wish to save the output figures, please create the following directories beforehand:

• figure/ - main figures
• supplemental/supp_fig/ - supplementary figures

Dependencies

This project uses Python 3.12.

To install the required packages, run:

pip install -r requirements.txt

Data

Due to size limitations, data files are not hosted on GitHub. They can be found via this Box Link

Contact

If you have questions, please email hurleyqi@utexas.edu.