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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Integration of Multiomic and Multi-phenotypic Data Identifies Biological Pathways Associated with Physical Fitness

ABSTRACT: Unraveling the complex associations between human phenotypes and molecular pathways can pave the way to improved health and performance, but faces a fundamental challenge: the measurable genes, proteins, and metabolites vastly outnumber the participants in even the largest studies, yielding spurious correlations. To address this, we developed PhenoMol, a bioinformatic framework that integrates comprehensive phenotypic data predictive of outcomes and reduces multi-omic dimensionality using graph theory constrained by prior biological knowledge. This approach generates biologically informed \"expression circuits\" to identify causal patterns. Applied to a deeply characterized healthy cohort, PhenoMol successfully predicted elite physical performance and outperformed regression models lacking network-based dimensionality reduction.

ORGANISM(S): Homo sapiens

SUBMITTER: Taisha Victoria Joseph-Risch

PROVIDER: E-MTAB-16584 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DNA Methylation Changes and Childhood Asthma in the Inner City [methylation]

Project description:Background: Epigenetic marks, like asthma, are heritable. They are influenced by the environment, direct the maturation of T cellslymphocytes, and have been shown to enhance the development of allergic airways disease in mice. Thus, we hypothesized that epigenetic marks are associated with allergic asthma in inner-city children. Methods: We compared methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy controls, using DNA and RNA from peripheral blood mononuclear cells (PBMCs) from inner city children aged 6-12 years with persistent atopic asthma children and healthy controls. Results were externally validated with the GABRIELA study population. Results: Comparing asthmatics (N=97) to controls (N=97), we identified 81 regions that were differentially methylated. Several immune genes were hypomethylated in asthmatics, including IL-13, RUNX3, and a number of specific genes relevant to natural killer cells (KIR2DL4, KIR2DL3, KIR3DL1, and KLRD1) and T cells lymphocytes (TIGIT). 14 differentially methylated regions (DMRs) were associated with the serum IgE concentration of IgE, including RUNX3. These results were internally and externally validated with a global methylation assessment using a different methodology in our inner-city cohort and an independent European cohort (GABRIELA). Hypo- and hypermethylated genes tended to be associated with increased and decreased gene expression, respectively (P<0.6x10-11 for asthma and ; P<0.01 for IgE). To further explore the relationship between methylation and gene expression, we created a matrix of genomic changes in methylation versus transcriptional changes (methyl eQTL) for asthma, and identified cis- and trans-regulated genes whose expression was related to asthma asthma-associated methylation marks. peripheral blood mononuclear cells (PBMCs) from 97 atopic asthmatic and 97 nonatopic nonasthmatic children

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2012-04-22 | E-GEOD-34008 | biostudies-arrayexpress

DNA Methylation Changes and Childhood Asthma in the Inner City

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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2022-12-31 | E-MTAB-12125 | biostudies-arrayexpress

DNA Methylation of gDNA from blood and bronchoalveolar lavage of tuburbulosis patients with and without type 2 diabetes via Illumina Infinium MethylationEPIC array

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