CRONDEX is a web-based platform developed to explore the relationships between chromatin-related genes and neurodevelopmental disorders (NDDs). This tool accompanies the research presented in Guerrero et al. (2026): "CRONDEX: a web-based platform for exploring links between chromatin-related genes and neurodevelopmental disorders".
The platform integrates data from SysNDD and EpiFactors to allow researchers to identify biologically coherent gene modules and formulate hypothesis-driven questions about the molecular basis of NDDs.
As described in the associated publication, CRONDEX features two primary query modes designed to navigate the phenotypic and functional landscape of NDD proteins:
From paralogs to functional modules. (App Tab: Single Gene Query)
This module enables users to identify chromatin-related NDD genes that share clinical features with a gene of interest. By leveraging phenotypic similarity (based on Human Phenotype Ontology annotations), this tool can uncover:
- Paralogous pairs with overlapping clinical presentations (e.g., CREBBP and EP300).
- Functionally convergent modules, such as the BAFopathies (SMARCA2, SMARCA4, etc.), where different genetic causes lead to similar syndromic outcomes.
Hypothesis-driven exploration. (App Tab: Criteria-Based Search)
This module allows users to filter the database based on specific functional and clinical criteria. It is designed to test hypotheses about the intersection of biological processes and disease phenotypes.
- Example Application: Exploring the intersection of "Intellectual Disability" with specific chromatin modifications (e.g., histone methylation) or metabolic pathways (e.g., thermogenesis), to identify potential molecular links between chromatin regulation and systemic phenotypes.
The easiest way to use CRONDEX is via the online version, which requires no installation:
If you prefer to run the application locally (e.g., for reproducible research or offline use), follow these steps:
- R (version 4.0 or higher)
- R packages listed in
requirements.txt
-
Clone the repository:
git clone https://github.com/yourusername/CRONDEX.git cd CRONDEX -
Install dependencies: You can install the required packages manually in R:
install.packages(c("shiny", "shinydashboard", "shinyWidgets", "DT", "tidyverse", "ggrepel", "visNetwork", "upsetjs")) # See requirements.txt for the full list
-
Run the App:
shiny::runApp()
If you use CRONDEX in your research, please cite:
Guerrero, J., Viegas, B.S., Martínez-Balbás, M., & de la Cruz, X. (2026). CRONDEX: a web-based platform for exploring links between chromatin-related genes and neurodevelopmental disorders. Research (VHIR), Universitat Autònoma de Barcelona.
This project is licensed under the MIT License - see the LICENSE file for details.