ArticleNPJ systems biology and applications2019
Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models.
Article in NPJ systems biology and applications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- Functional Profiling of Soft Tissue Sarcoma Using Mechanistic Models.International journal of molecular sciences · 2023Article
- Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer.International journal of molecular sciences · 2023Article
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- Toward modeling metabolic state from single-cell transcriptomics.Molecular metabolism · 2022Review
- Potential Diagnostic and Prognostic Values of CBX8 Expression in Liver Hepatocellular Carcinoma, Kidney Renal Clear Cell Carcinoma, and Ovarian Cancer: A Study Based on TCGA Data Mining.Computational and mathematical methods in medicine · 2022Article
- Targeting of the Lipid Metabolism Impairs Resistance to BRAF Kinase Inhibitor in Melanoma.Frontiers in cell and developmental biology · 2022Article
- Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.Frontiers in oncology · 2022Review
- Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures.NPJ systems biology and applications · 2021Article
- Opposed Interplay between IDH1 Mutations and the WNT/β-Catenin Pathway: Added Information for Glioma Classification.Biomedicines · 2021Review
- The Glioblastoma Microenvironment: Morphology, Metabolism, and Molecular Signature of Glial Dynamics to Discover Metabolic Rewiring Sequence.International journal of molecular sciences · 2021Review
- Incorporating Machine Learning into Established Bioinformatics Frameworks.International journal of molecular sciences · 2021Review
- Mechanistic modeling of the SARS-CoV-2 disease map.BioData mining · 2021Article
- Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology.Briefings in bioinformatics · 2021Review
- Article
- Article
- Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape.NAR cancer · 2020Article
- A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders.Frontiers in bioengineering and biotechnology · 2020Article
- Using mechanistic models for the clinical interpretation of complex genomic variation.Scientific reports · 2019Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In spite of the increasing availability of genomic and transcriptomic data, there is still a gap between the detection of perturbations in gene expression and the understanding of their contribution to the molecular mechanisms that ultimately account for the phenotype studied. Alterations in the metabolism are behind the initiation and progression of many diseases, including cancer. The wealth of available knowledge on metabolic processes can therefore be used to derive mechanistic models that link gene expression perturbations to changes in metabolic activity that provide relevant clues on molecular mechanisms of disease and drug modes of action (MoA). In particular, pathway modules, which recapitulate the main aspects of metabolism, are especially suitable for this type of modeling. We present Metabolizer, a web-based application that offers an intuitive, easy-to-use interactive interface to analyze differences in pathway metabolic module activities that can also be used for class prediction and in silico prediction of knock-out (KO) effects. Moreover, Metabolizer can automatically predict the optimal KO intervention for restoring a diseased phenotype. We provide different types of validations of some of the predictions made by Metabolizer. Metabolizer is a web tool that allows understanding molecular mechanisms of disease or the MoA of drugs within the context of the metabolism by using gene expression measurements. In addition, this tool automatically suggests potential therapeutic targets for individualized therapeutic interventions.
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