ceRNAxis

Welcome to the official documentation of ceRNAxis!

Overview

ceRNAxis detects ceRNA network LncRNA-miRNA-mRNA triplet axis from RNA expression profiles.

We have manually curated a reference ceRNA network 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 ceRNAxis with full reference ceRNA network, please download the full file ceRNA_ref.csv, and place it into cernatax/data.

Getting Started

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

Tutorial Guide

The followings are AS Paper scripts on how to use ceRNAxis on the SCZ and GDM cohort:

• Basic operations and stats for the reference ceRNA network
• SCZ - Use DEG to get cohort-specific and disease relatated ceRNA axis from SCZ data
• GDM - Use DEG to get cohort-specific and disease relatated ceRNA axis from GDM data
• SCZ - ceRNA expression visualization for a cohort
• SCZ - ceRNA-axis correlation analysis for a cohort
• SCZ - GWAS analysis for ceRNA-axis

Citation

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

X. Gong, L. Chen, X. Guo, et al. LncRNA THUMPD3-AS1 Regulates Behavioral and Synaptic Structural Abnormalities in Schizophrenia via miR-485-5p and ARHGAP8. Adv. Sci. (2025): e08867. https://doi.org/10.1002/advs.202508867

BibTeX format:

@article{https://doi.org/10.1002/advs.202508867,
author = {Gong, Xiaojuan and Chen, Lingxi and Guo, Xin and Jiang, Anna and He, Yayi and Yan, Chunxia and Ma, Liang and Gao, Jiayang and Zhang, Jinyu and Zhang, Bao},
title = {LncRNA THUMPD3-AS1 Regulates Behavioral and Synaptic Structural Abnormalities in Schizophrenia via miR-485-5p and ARHGAP8},
journal = {Advanced Science},
pages = {e08867},
keywords = {noncoding RNA regulation, Rho GTPase signaling, schizophrenia, synaptic pathology},
doi = {https://doi.org/10.1002/advs.202508867},
url = {https://advanced.onlinelibrary.wiley.com/doi/abs/10.1002/advs.202508867},
}