ArticleScientific reports2016
Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD.Nature communications · 2025Article
- 5G-exposed human skin cells do not respond with altered gene expression and methylation profiles.PNAS nexus · 2025Article
- Identifying metabolic shifts in Crohn's disease using' omics-driven contextualized computational metabolic network models.Scientific reports · 2023Article
- Network location and clustering of genetic mutations determine chronicity in a stylized model of genetic diseases.Scientific reports · 2022Article
- Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study.Human genomics · 2022Article
- Two classes of functional connectivity in dynamical processes in networks.Journal of the Royal Society, Interface · 2021Article
- A hexokinase isoenzyme switch in human liver cancer cells promotes lipogenesis and enhances innate immunity.Communications biology · 2021Article
- Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease.Frontiers in genetics · 2021Review
- Review
- A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli.PLoS computational biology · 2019Article
- Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.Metabolites · 2019Article
- The metabolic network coherence of human transcriptomes is associated with genetic variation at the cadherin 18 locus.Human genetics · 2019Article
- An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease.BMC bioinformatics · 2018Article
- The Impact of Western Diet and Nutrients on the Microbiota and Immune Response at Mucosal Interfaces.Frontiers in immunology · 2017Review
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5 authors.
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Abstract
Information on biological networks can greatly facilitate the function-orientated interpretation of high-throughput molecular data. Genome-wide metabolic network models of human cells, in particular, can be employed to contextualize gene expression profiles of patients with the goal of both, a better understanding of individual etiologies and an educated reclassification of (clinically defined) phenotypes. We analyzed publicly available expression profiles of intestinal tissues from treatment-naive pediatric inflammatory bowel disease (IBD) patients and age-matched control individuals, using a reaction-centric metabolic network derived from the Recon2 model. By way of defining a measure of 'coherence', we quantified how well individual patterns of expression changes matched the metabolic network. We observed a bimodal distribution of metabolic network coherence in both patients and controls, albeit at notably different mixture probabilities. Multidimensional scaling analysis revealed a bisectional pattern as well that overlapped widely with the metabolic network-based results. Expression differences driving the observed bimodality were related to cellular transport of thiamine and bile acid metabolism, thereby highlighting the crosstalk between metabolism and other vital pathways. We demonstrated how classical data mining and network analysis can jointly identify biologically meaningful patterns in gene expression data.
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