ArticleBMC bioinformatics2018
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 175 papers, 1 of them a synthesis that pooled it.
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Who cites it
175 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- A Systems Vaccinology Approach Reveals the Mechanisms of Immunogenic Responses to Hantavax Vaccination in Humans.Scientific reports · 2019Trial
- Inflammation induced by influenza virus impairs human innate immune control of pneumococcus.Nature immunology · 2018Trial
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- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
- Multi-Network Co-expression Analysis Enhances Biological Insights from Single-Cell Gene Expression.Interdisciplinary sciences, computational life sciences · 2026Article
- Transcription-based comparison ofMicrobiology spectrum · 2026Article
- Combined Photothermal and mTOR-Targeted Therapy Overcomes Immune Evasion and Enhances Checkpoint Blockade Efficacy in Metastatic Triple-Negative Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.Briefings in bioinformatics · 2026Article
- Temporal transcriptional dynamics in cutaneous leishmaniasis reveal novel targets for therapeutic interventions in a dermal mouse model.Frontiers in immunology · 2026Article
- Metabolite coupling analysis and metabolite-flux coupling analysis of genome-scale metabolic models.Frontiers in bioinformatics · 2026Article
- Distinct immune responses to HIV and CMV in Hofbauer cells across gestation highlight evolving placental immune dynamics.Frontiers in immunology · 2026Article
- Persistent pneumococcal colonisation in antiretroviral-treated HIV infection is associated with nasal inflammation.Nature communications · 2025Article
- Data-driven discovery of gene expression markers distinguishing pediatric acute lymphoblastic leukemia subtypes.Molecular oncology · 2025Article
- Inflammatory Biomarkers of Asymptomatic and Symptomatic Tuberculosis.bioRxiv : the preprint server for biology · 2025Article
115 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
Abstract
backgroundThe analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the discovery of clinically relevant molecular pathways underlying different diseases and conditions.
resultsIn this paper, we present a fast and easy-to-use Bioconductor package named CEMiTool that unifies the discovery and the analysis of co-expression modules. Using the same real datasets, we demonstrate that CEMiTool outperforms existing tools, and provides unique results in a user-friendly html report with high quality graphs. Among its features, our tool evaluates whether modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group, as well as it integrates transcriptomic data with interactome information, identifying the potential hubs on each network. We successfully applied CEMiTool to over 1000 transcriptome datasets, and to a new RNA-seq dataset of patients infected with Leishmania, revealing novel insights of the disease's physiopathology.
conclusionThe CEMiTool R package provides users with an easy-to-use method to automatically implement gene co-expression network analyses, obtain key information about the discovered gene modules using additional downstream analyses and retrieve publication-ready results via a high-quality interactive report.
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