ArticleBioinformatics (Oxford, England)2012
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 259 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
259 citing papers in PubMed, 1 synthesis or guideline pooled it, 430 citations in OpenAlex.
- Paediatric obesity: a systematic review and pathway mapping of metabolic alterations underlying early disease processes.Molecular medicine (Cambridge, Mass.) · 2021Pooled it
- Metabolomics and cancer preventive behaviors in the BC Generations Project.Scientific reports · 2021Trial
- Metabolomic change due to combined treatment with myo-inositol, D-chiro-inositol and glucomannan in polycystic ovarian syndrome patients: a pilot study.Journal of ovarian research · 2019Trial
- Integrated transcriptomic and metabolomic analyses reveal host-metabolite interactions underlying cloacal inflammation in laying Pekin ducks.Animal bioscience · 2026Article
- Lactobacillus gasseri alleviates type 2 diabetes via modulation of gut microbiota-host metabolic networks.Journal of endocrinological investigation · 2026Article
- MAPA: A Semantic Network Framework for Functional Module Discovery and Interpretation in Multi-Omics Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Beyond Metabolism: Pyruvate Carboxylase Acts as a Sequence-Selective Small RNA Sensor Orchestrating Antiviral Responses.bioRxiv : the preprint server for biology · 2026Article
- Article
- hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models.Bioinformatics (Oxford, England) · 2026Article
- Integrated multi-omics and single-cell analyses identify metabolic heterogeneity and therapeutic vulnerabilities in medullary thyroid cancer.British journal of cancer · 2026Article
- Article
- Microbiota dysbiosis influences immune system and muscle pathophysiology of dystrophin deficient mice.EMBO molecular medicine · 2026Article
- Spleen Metabolome Reveals Immune-Mediated Responses Modulated by Onion Peel Extract inMicroorganisms · 2026Article
- PMconv: How to Compare Proteomes and Metabolomes?International journal of molecular sciences · 2026Article
- Circulating metabolites associated with protection against Mycobacterium tuberculosis infection and inhibition of mycobacterial growth.Communications biology · 2026Article
- Urinary GC-MS metabolomics reveals pregnancy-associated metabolic reprogramming and biomarkers in buffaloes.BMC veterinary research · 2026Article
- Age-Associated Metabolomic Changes in Human Spermatozoa.International journal of molecular sciences · 2026Article
- Comprehensive metabolic profiling uncovers early variation and biomarkers of esophageal squamous cell carcinoma.Science China. Life sciences · 2026Article
- Analyzing Plant Low-Molecular-Weight Polar Metabolites: A GC-MS Approach.Plants (Basel, Switzerland) · 2026Review
- Hybrid Feature Selection-Based Machine Learning and Deep Learning Framework for Biomarker Prediction From RNA-seq Data During Dengue Fever to Severe Dengue Progression.Evolutionary bioinformatics online · 2026Article
199 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 1 institution in 2 countries.
Funding
Abstract
motivationMetabolomics is a rapidly evolving field that holds promise to provide insights into genotype-phenotype relationships in cancers, diabetes and other complex diseases. One of the major informatics challenges is providing tools that link metabolite data with other types of high-throughput molecular data (e.g. transcriptomics, proteomics), and incorporate prior knowledge of pathways and molecular interactions.
resultsWe describe a new, substantially redesigned version of our tool Metscape that allows users to enter experimental data for metabolites, genes and pathways and display them in the context of relevant metabolic networks. Metscape 2 uses an internal relational database that integrates data from KEGG and EHMN databases. The new version of the tool allows users to identify enriched pathways from expression profiling data, build and analyze the networks of genes and metabolites, and visualize changes in the gene/metabolite data. We demonstrate the applications of Metscape to annotate molecular pathways for human and mouse metabolites implicated in the pathogenesis of sepsis-induced acute lung injury, for the analysis of gene expression and metabolite data from pancreatic ductal adenocarcinoma, and for identification of the candidate metabolites involved in cancer and inflammation. AVAILABILITY: Metscape is part of the National Institutes of Health-supported National Center for Integrative Biomedical Informatics (NCIBI) suite of tools, freely available at http://metscape.ncibi.org. It can be downloaded from http://cytoscape.org or installed via Cytoscape plugin manager. CONTACT: metscape-help@umich.edu; akarnovs@umich.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.