ArticleScientific reports2021
Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Inflamed Yet Immune-Evasive? A Transcriptomic Meta-Analysis Identifies Conserved Inflammatory, Developmental, and Neuronal Signatures Associated with Polyploid Giant Cancer Cells.International journal of molecular sciences · 2026Pooled it
- An integrative approach to identify novel miRNA-mRNA interaction networks in LMNA-cardiomyopathy.Scientific reports · 2026Article
- Elucidating molecular mechanisms of allergic sensitization to olive pollen through transcriptomics.Frontiers in immunology · 2026Article
- Revealing the complexity of the epicardial secretome.Scientific reports · 2025Article
- Integrative Transcriptomic and Network-Based Analysis of Neuromuscular Diseases.International journal of molecular sciences · 2025Article
- β-Hydroxybutyrate Reduces Body Weight by Modulating Fatty Acid Oxidation and Beiging in the Subcutaneous Adipose Tissue of DIO Mice.International journal of molecular sciences · 2025Article
- Cytokine profiling and transcriptomics in mononuclear cells define immune variants in Meniere Disease.Genes and immunity · 2024Article
- Exploring miRNA-target gene pair detection in disease with coRmiT.Briefings in bioinformatics · 2024Article
- Key anti-freeze genes and pathways of Lanzhou lily (Lilium davidii, var. unicolor) during the seedling stage.PloS one · 2024Article
- Advancing in Schaaf-Yang syndrome pathophysiology: from bedside to subcellular analyses of truncated MAGEL2.Journal of medical genetics · 2023Article
- SpPdp11 Administration in Diet Modified the Transcriptomic Response and Its Microbiota Associated in Mechanically Induced WoundAnimals : an open access journal from MDPI · 2023Article
- Revealing genetic links of Type 2 diabetes that lead to the development of Alzheimer's disease.Heliyon · 2023Article
- Transcriptional changes in dendritic cells underlying allergen specific induced tolerance in a mouse model.Scientific reports · 2022Article
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Authors and funding
10 authors.
Funding
Abstract
High-throughput gene expression analysis is widely used. However, analysis is not straightforward. Multiple approaches should be applied and methods to combine their results implemented and investigated. We present methodology for the comprehensive analysis of expression data, including co-expression module detection and result integration via data-fusion, threshold based methods, and a Naïve Bayes classifier trained on simulated data. Application to rare-disease model datasets confirms existing knowledge related to immune cell infiltration and suggest novel hypotheses including the role of calcium channels. Application to simulated and spike-in experiments shows that combining multiple methods using consensus and classifiers leads to optimal results. ExpHunter Suite is implemented as an R/Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite . It can be applied to model and non-model organisms and can be run modularly in R; it can also be run from the command line, allowing scalability with large datasets. Code and reports for the studies are available from https://github.com/fmjabato/ExpHunterSuiteExamples .
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