CERNATAX

Welcome to the official documentation of CERNATAX!

Overview

CERNATAX detects ceRNA network mRNA-miRNA-lncRNA triplet axis from RNA expression profiles.

We have manually curated a ceRNA network database by integrating TargetSCAN 8.0, miRTarBase 9.0, miRDB 6.0, NPInter 4.0, ENCORI/starBase 2.0, miRWalk V3, and RNAInter in 2020.

To run CERNATAX with full reference ceRNA network, please download the full db file ceRNA_database.csv, and place it into cernatax/db.

Getting Started

Want to start using it immediately? Check out the Installation Guide.

Tutorial Guide

The followings are tutorials of how to use CERNATAX on the SCZ cohort:

• Basic operations and stats for the reference ceRNA network
• Use DEG to get cohort-specific and disease relatated ceRNA axis
• ceRNA expression visualization for a cohort
• ceRNA-axis correlation analysis for a cohort
• Predict disease phenotype using ceRNA axis

Citation

If you use CERNATAX in your research, please cite the following paper:

APA format:

Liu, X., Jiang, A., Lyu, C., & Chen, L. (2025). Knowledge-driven annotation for gene interaction enrichment analysis. bioRxiv, 2025-04. https://doi.org/10.1101/2025.04.15.649030

BibTeX format:

@article{grea,
  title={Knowledge-driven annotation for gene interaction enrichment analysis},
  author={Liu, Xiaoyu and Jiang, Anna and Lyu, Chengshang and Chen, Lingxi},
  journal={bioRxiv},
  pages={2025--04},
  year={2025},
  doi={10.1101/2025.04.15.649030},
  publisher={Cold Spring Harbor Laboratory}
}