webCEMiTool: Co-expression modular analysis made easy
Lucas E. Cardozo1, 
Pedro S. Russo1, Bruno Gomes-Correia2,
Mariana Araujo-Pereira3, 
Gonzalo Sepúlveda-Hermosilla4, 
Vinicius Maracaja-Coutinho2 and 
Helder I. Nakaya1* - 1Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
- 2Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Chile
- 3Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
- 4Centro de Genómica y Bioinformática, Universidad Mayor, Chile
Co-expression analysis has been widely used to elucidate the functional architecture of genes under different biological processes. Such analysis, however, requires substantial knowledge about programming languages and/or bioinformatics skills. We present webCEMiTool (https://cemitool.sysbio.tools/), a unique online tool that performs comprehensive modular analyses in a fully automated manner. The webCEMiTool not only identifies co-expression gene modules, but it also performs several functional analyses on them. In addition, webCEMiTool integrates transcriptomic data with interactome information (i.e. protein-protein interactions), and identifies potential hubs on each network. The tool generates user-friendly html reports that allow users to search for specific genes in each module, as well as check if a module contains genes over-represented in specific pathways or altered in a specific sample phenotype. We used webCEMiTool to perform a modular analysis of single-cell RNA-seq data of human cells infected with either Zika virus or Dengue virus.
Keywords: Co-expression analysis, systems biology, Transcriptomics, Web tool, data integration
Received: 29 Aug 2018;
Accepted: 12 Feb 2019.
Edited by:
Akira Funahashi, Keio University, JapanReviewed by:
Marco Vanoni, University of Milano-Bicocca, ItalyTakahiro G. Yamada, Keio University, Japan
Copyright: © 2019 Cardozo, Russo, Gomes-Correia, Araujo-Pereira, Sepúlveda-Hermosilla, Maracaja-Coutinho and Nakaya. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Dr. Helder I. Nakaya, Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, 05508, Sao Paulo, Brazil, hnakaya@usp.br
