Dataset Information

Perseus plugin "Metis" for metabolic-pathway-centered quantitative multi-omics data analysis for static and time-series experimental designs.

ABSTRACT: We introduce Metis, a new plugin for the Perseus software aimed at analyzing quantitative multi-omics data based on metabolic pathways. Data from different omics types are connected through reactions of a genome-scale metabolic-pathway reconstruction. Metabolite concentrations connect through the reactants, while transcript, protein, and protein post-translational modification (PTM) data are associated through the enzymes catalyzing the reactions. Supported experimental designs include static comparative studies and time-series data. As an example for the latter, we combine circadian mouse liver multi-omics data and study the contribution of cycles of phosphoproteome and metabolome to enzyme activity regulation. Our analysis resulted in 52 pairs of cycling phosphosites and metabolites connected through a reaction. The time lags between phosphorylation and metabolite peak show non-uniform behavior, indicating a major contribution of phosphorylation in the modulation of enzymatic activity.

SUBMITTER: Hamzeiy H

PROVIDER: S-EPMC9046241 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Perseus plugin "Metis" for metabolic-pathway-centered quantitative multi-omics data analysis for static and time-series experimental designs.

Hamzeiy Hamid H Ferretti Daniela D Robles Maria S MS Cox Jürgen J

Cell reports methods 20220414 4

We introduce Metis, a new plugin for the Perseus software aimed at analyzing quantitative multi-omics data based on metabolic pathways. Data from different omics types are connected through reactions of a genome-scale metabolic-pathway reconstruction. Metabolite concentrations connect through the reactants, while transcript, protein, and protein post-translational modification (PTM) data are associated through the enzymes catalyzing the reactions. Supported experimental designs include static co ...[more]

PMID: 35497496

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Project description:BACKGROUND:Nonadherence to medications by patients requiring hemodialysis (HD) leads to unfavorable clinical outcomes. Limited data exist to demonstrate the effect of incorporating patient-centered interventions using concepts of medication therapy management and motivational interview by pharmacists on pharmacoadherence in patients requiring HD. Therefore, we assessed the impact of patient-centered pharmacist care on pharmacoadherence and its outcomes in patients requiring HD. METHODS:Adult patients who had received outpatient HD for at least 3 months were enrolled. The study was conducted from October 2016 to April 2017. Pharmacists interviewed the patients at month 1, 2, 4 and 6, and the intervention (comprehensive review) occurred at months 3 and 5. The primary outcome was the change in pharmacoadherence as assessed by pre-HD serum phosphate levels and the differences in the number of medications between patient' self-report and medications records at the electronic healthcare records (EHRs). The secondary outcomes included changes in systolic blood pressure (SBP), glycosylated hemoglobin levels, serum low-density lipoprotein (LDL) levels, and the prevalence and types of medication-related problems (MRPs). RESULTS:Seventy-two patients were enrolled. Their median age was 59 (interquartile range: 47-67.5) years, and 53% were men. Pre- and post-intervention pharmacoadherence, as indicated by serum phosphate levels and the differences in the number of medications between patient' self-report and the medication records at the EHRs, did not significantly differ (p = 0.682 and 0.348, respectively). Mean SBP and mean LDL did not significantly change post-intervention. The median number of MRPs declined between Months 3 and 5 (p = 0.002): the prevalence of MRPs at Month 3 was 44.9% (95 confidence interval [CI]: 40.4-49.3) and decreased to 29.8% (95 CI: 25.6-34.3) at Month 5. Drug use without indication was the most frequent MRP (23.9%). CONCLUSIONS:Patient-centered pharmacist care did not result in significant changes in pharmacoadherence. However, its clinical utility as a tool to identify and mitigate MRPs in patients requiring HD is indisputable. TRIAL REGISTRATION:ClinicalTrials.gov identifier: NCT03576404 (retrospectively registered on July 3rd, 2018).

Dataset Information

Perseus plugin "Metis" for metabolic-pathway-centered quantitative multi-omics data analysis for static and time-series experimental designs.

Publications

Perseus plugin "Metis" for metabolic-pathway-centered quantitative multi-omics data analysis for static and time-series experimental designs.

Similar Datasets

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