ArticleNucleic acids research2022
PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 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
55 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Metabolomics and metabolites in cancer diagnosis and treatment.Molecular biomedicine · 2025Pooled it
- Comparison ofMicrobiology (Reading, England) · 2026Article
- Multi-omics integration of proteomics and metabolomics in pediatric health and disease.Communications medicine · 2026Review
- Hyperspectral imaging reveals early drought stress and associated molecular responses in lettuce for space agriculture.Plant phenomics (Washington, D.C.) · 2026Article
- Improving recombinant protein productivity in CHO cells via multi-omics data integration.Bioresources and bioprocessing · 2026Review
- Integrated Multiomics Enabled by Sequential Extraction for Comprehensive Molecular Profiling of Small Extracellular Vesicles.Analytical chemistry · 2026Article
- PMconv: How to Compare Proteomes and Metabolomes?International journal of molecular sciences · 2026Article
- Ole-4, a novel synthetic derivative of Oleuropein, enhances antitumor immunity and modulates kinase activity-dependent signaling.Journal of translational medicine · 2026Article
- OmNI: a modular open-source framework for interactive multi-omics data integration and visualization.NAR genomics and bioinformatics · 2026Article
- Challenges and Opportunities in Multi-Omics Data Acquisition and Analysis: Toward Integrative Solutions.Biomolecules · 2026Review
- Unlocking the power of extracellular vesicles: multi-omics integration for cancer biomarker discovery.Biomarker research · 2026Review
- Mass Spectrometry Proteomics: A Key to Faster Drug Discovery.Journal of medicinal chemistry · 2026Review
- Multi-omics strategies for biomarker discovery and application in personalized oncology.Molecular biomedicine · 2025Review
- Metabolomics and Pharmacometabolomics: Advancing Precision Medicine in Drug Discovery and Development.Metabolites · 2025Review
- NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline.Bioinformatics (Oxford, England) · 2025Article
- Alveolar Epithelial Cell Dysfunction in Acute Respiratory Distress Syndrome: Mechanistic Insights and Targeted Interventions.Biomedicines · 2025Review
- Spatial transcriptomics delineates potential differences in intestinal phenotypes of cardiac and classical necrotizing enterocolitis.iScience · 2025Article
- Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato.Plant physiology · 2025Article
- Article
- Biosynthesis of bromoform byBiotechnology reports (Amsterdam, Netherlands) · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology. PaintOmics 4 is available at https://paintomics.org/.
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.