ReviewBriefings in bioinformatics2022
A comprehensive survey of the approaches for pathway analysis using multi-omics data integration.
Review in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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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.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-omics approaches to deciphering complex pathological mechanisms of migraine: a systematic review.Frontiers in pharmacology · 2024Pooled it
- Multiomics Insights Linking Personal Care Products Exposure to Serum Lipid Profiles in Older Adults: The China BAPE Study.Environmental health perspectives · 2026Article
- Reconstructing bovine disease trajectories through integrative multi-omics: molecular decision nodes, predictive biomarkers and precision intervention.Veterinary research communications · 2026Review
- Knowledge-driven interpretable neural networks provide mechanistic insight.Genome research · 2026Article
- DeOPUS: cellular deconvolution via optimized power-transformed unmixing with shrinkage.Briefings in bioinformatics · 2026Article
- AI and network biology for rational polypharmacology in signaling drug design: a review.NPJ precision oncology · 2026Review
- Assessing current capabilities for incorporating lipidomics in multiomics data integration.Briefings in bioinformatics · 2026Review
- The crosstalk between epigenetics and metabolism in the malignant cell.Discover oncology · 2026Review
- Comprehensive Insights into Natural Bioactive Compounds: From Chemical Diversity and Mechanisms to Biotechnological Innovations and Applications.ChemistryOpen · 2026Review
- Integrated multi-omics reveals coordinatedmSystems · 2026Article
- Multiomics approaches in Kawasaki disease: insights into pathogenesis and emerging directions for diagnosis and treatment.Clinical and experimental pediatrics · 2026Article
- A comparative study of the gut microbiome and fecal metabolome in hypertensive patients from middle-temperate and tropical cities of China: Daqing and Haikou.Frontiers in microbiology · 2026Article
- MPAC: a computational framework for inferring pathway activities from multi-omic data.Bioinformatics (Oxford, England) · 2025Article
- The Future of a Myriad of Accelerated Biodiscoveries Lies in AI-Powered Mass Spectrometry and Multiomics Integration.Journal of mass spectrometry : JMS · 2025Article
- Pathway Analysis Interpretation in the Multi-Omic Era.Biotech (Basel (Switzerland)) · 2025Review
- Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol-Related Liver Disease.Journal of cachexia, sarcopenia and muscle · 2025Article
- Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.BMC genomics · 2025Article
- Article
- A comprehensive review of cancer survival prediction using multi-omics integration and clinical variables.Briefings in bioinformatics · 2025Review
- Genome-wide association study of chlamydia reinfection in African American women.Frontiers in immunology · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Pathway analysis has been widely used to detect pathways and functions associated with complex disease phenotypes. The proliferation of this approach is due to better interpretability of its results and its higher statistical power compared with the gene-level statistics. A plethora of pathway analysis methods that utilize multi-omics setup, rather than just transcriptomics or proteomics, have recently been developed to discover novel pathways and biomarkers. Since multi-omics gives multiple views into the same problem, different approaches are employed in aggregating these views into a comprehensive biological context. As a result, a variety of novel hypotheses regarding disease ideation and treatment targets can be formulated. In this article, we review 32 such pathway analysis methods developed for multi-omics and multi-cohort data. We discuss their availability and implementation, assumptions, supported omics types and databases, pathway analysis techniques and integration strategies. A comprehensive assessment of each method's practicality, and a thorough discussion of the strengths and drawbacks of each technique will be provided. The main objective of this survey is to provide a thorough examination of existing methods to assist potential users and researchers in selecting suitable tools for their data and analysis purposes, while highlighting outstanding challenges in the field that remain to be addressed for future development.
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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.