Dataset Information

COMMO: A web server for the identification and analysis of consensus gene modules across multiple methods.

ABSTRACT:

Summary

A variety of computational methods have been developed to identify functionally related gene modules from genome-wide gene expression profiles. Integrating the results of these methods to identify consensus modules is a promising approach to produce more accurate and robust results. In this application note, we introduce COMMO, the first web server to identify and analyze consensus gene functionally related gene modules from different module detection methods. First, COMMO implements eight state-of-the-art module detection methods and two consensus clustering algorithms. Second, COMMO provides users with mRNA and protein expression data for 33 cancer types from three public databases. Users can also upload their own data for module detection. Third, users can perform functional enrichment and two types of survival analyses on the observed gene modules. Finally, COMMO provides interactive, customizable visualizations and exportable results. With its extensive analysis and interactive capabilities, COMMO offers a user-friendly solution for conducting module-based precision medicine research.

Availability and implementation

COMMO web is available at https://commo.ncpsb.org.cn/, with the source code available on GitHub: https://github.com/Song-xinyu/COMMO/tree/master.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Wu X

PROVIDER: S-EPMC10713113 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Publications

COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods.

Wu Xiaojing X Han Mingfei M Song Xinyu X He Song S Bo Xiaochen X Zhu Yunping Y

Bioinformatics (Oxford, England) 20231201 12

<h4>Summary</h4>A variety of computational methods have been developed to identify functionally related gene modules from genome-wide gene expression profiles. Integrating the results of these methods to identify consensus modules is a promising approach to produce more accurate and robust results. In this application note, we introduce COMMO, the first web server to identify and analyze consensus gene functionally related gene modules from different module detection methods. First, COMMO implem ...[more]

PMID: 37995293

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