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Updated: Jun 14, 2025

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

XGRm: A Web Server for Interpreting Mouse Summary-level Genomic Data.

Shan Wang¹, Chaohui Bao¹, Siyue Yang²

¹Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.

Journal of Molecular Biology

|September 5, 2024

Summary

This summary is machine-generated.

We present XGR-model (XGRm), a web server for analyzing mouse genomic data. It provides tools for enrichment and subnetwork analysis, aiding systems biology insights from summary-level genomic data.

Keywords:

enrichment analysis genomic data model organism mouse subnetwork analysis

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Area of Science:

Genomics
Systems Biology
Bioinformatics

Background:

Interpreting summary-level genomic data in model organisms is challenging.
Existing tools may not offer comprehensive analysis for mouse genomic datasets.

Purpose of the Study:

Introduce XGR-model (XGRm), a web server for analyzing mouse genomic data.
Provide integrated tools for enrichment and subnetwork analysis of gene-centric and region-centric data.

Main Methods:

Developed XGR-model (XGRm) web server accessible at http://www.xgrm.pro.
Integrated GElyser and RElyser for ontology term enrichment analysis.
Implemented GSlyser and RSlyser for gene and region-centric subnetwork analysis using network algorithms.

Main Results:

XGRm offers four analysers: two for enrichment and two for subnetwork analysis.
Supports both gene-centric and genomic region-centric mouse data.
Leverages functional and pathway-derived interaction networks for analysis.

Conclusions:

XGRm provides an all-in-one solution for systems biology insights from mouse genomic data.
The platform is designed for regular updates and potential extensions to other model organisms.