ArticleScientific reports2015
Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- Genome-scale metabolic modeling uncovers cell-type specific signatures associated with APOE variants.iScience · 2026Article
- In vivo and in silico models of Drosophila for Parkinson's disease.The FEBS journal · 2025Review
- A personalized metabolic modelling approach through integrated analysis of RNA-Seq-based genomic variants and gene expression levels in Alzheimer's disease.Communications biology · 2025Article
- Multilayer Analysis of RNA Sequencing Data in Alzheimer's Disease to Unravel Molecular Mysteries.Advances in neurobiology · 2024Review
- Integrated small RNA, mRNA and protein omics reveal a miRNA network orchestrating metabolic maturation of the developing human heart.BMC genomics · 2023Article
- Transcriptome data analysis of primary cardiomyopathies reveals perturbations in arachidonic acid metabolism.Frontiers in cardiovascular medicine · 2023Article
- Network-based metabolic characterization of renal cell carcinoma.Scientific reports · 2020Article
- Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epithelial cells with metabolic and protein-protein interaction networks.Turkish journal of biology = Turk biyoloji dergisi · 2020Article
- Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine.Frontiers in bioengineering and biotechnology · 2020Review
- Metabolite-Centric Reporter Pathway and Tripartite Network Analysis ofFrontiers in bioengineering and biotechnology · 2018Article
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Authors and funding
1 author.
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Abstract
A systems-based investigation of the effect of perturbations on metabolic machinery is crucial to elucidate the mechanism behind perturbations. One way to investigate the perturbation-induced changes within the cell metabolism is to focus on pathway-level effects. In this study, three different perturbation types (genetic, environmental and disease-based) are analyzed to compute a list of reporter pathways, metabolic pathways which are significantly affected from a perturbation. The most common omics data type, transcriptome, is used as an input to the bioinformatic analysis. The pathways are scored by two alternative approaches: by averaging the changes in the expression levels of the genes controlling the associated reactions (reaction-centric), and by averaging the changes in the associated metabolites which were scored based on the associated genes (metabolite-centric). The analysis reveals the superiority of the novel metabolite-centric approach over the commonly used reaction-centric approach since it is based on metabolites which better represent the cross-talk among different pathways, enabling a more global and realistic cataloguing of network-wide perturbation effects.
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