ArticleNature communications2024
Directional integration and pathway enrichment analysis for multi-omics data.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 2 of them syntheses that pooled it.
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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
28 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Predictive enrichment using biomarkers in studies of critically-ill patients with sepsis: a systematic review.Critical care (London, England) · 2025Pooled it
- Metabolomics and metabolites in cancer diagnosis and treatment.Molecular biomedicine · 2025Pooled it
- Emerging natural product development strategies drive the therapeutic potential exploration and clinical translation of hydroxysafflor yellow A.Journal of pharmaceutical analysis · 2026Review
- Biochemically Constrained Multi-Omics Integration Reveals Protein-Metabolite Dependencies Across Diseases.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrated multi-omics analysis identifies potential therapeutic targets for Alzheimer's disease.Neural regeneration research · 2026Article
- The microbial unknome, a repertoire for microbial chatting?Heredity · 2026Review
- Target primacy, inference robustness, and translational causality in ferroptosis-based immunotherapy combinations.International journal of surgery (London, England) · 2026Article
- Omics Data Integration: Focusing on Molecular Biomarkers for Cancers and Diseases.Biomolecules · 2026Article
- Natural variation inScience advances · 2026Article
- Profiling of extracellular vesicles from primary hepatocytes, organoids, and mash patients identifies cell injury-specific signatures.Scientific reports · 2026Article
- Assessing current capabilities for incorporating lipidomics in multiomics data integration.Briefings in bioinformatics · 2026Review
- Benchmarking computational methods for multi-omics biomarker discovery in cancer.Briefings in bioinformatics · 2026Article
- Tissue-layer-resolved proteome landscape of Crohn's disease strictures highlights potential drivers of fibrosis progression.JCI insight · 2026Article
- DNMT3A R882H Is Not Required for Disease Maintenance in Primary Human AML but Is Associated with Increased Leukemia Stem Cell Frequency.Cancer discovery · 2026Article
- A proteogenomic atlas of 1032 brain metastases identifies molecular subtypes, immune landscapes, and therapeutic vulnerabilities.Nature communications · 2026Article
- Mass Spectrometry Proteomics: A Key to Faster Drug Discovery.Journal of medicinal chemistry · 2026Review
- Computational Methods for Pathway and Network Analysis with MicroRNAs.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Cancer Genomic Alterations and Microenvironmental Features Encode Synergistic Interactions with Disease Outcomes.Molecular cancer research : MCR · 2025Article
- Topoisomerase IIb binding delineates localized mutational processes and driver mutations in cancer genomes.Nature communications · 2025Article
- Statistical Methods for Multi-Omics Analysis in Neurodevelopmental Disorders: From High Dimensionality to Mechanistic Insight.Biomolecules · 2025Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Omics techniques generate comprehensive profiles of biomolecules in cells and tissues. However, a holistic understanding of underlying systems requires joint analyses of multiple data modalities. We present DPM, a data fusion method for integrating omics datasets using directionality and significance estimates of genes, transcripts, or proteins. DPM allows users to define how the input datasets are expected to interact directionally given the experimental design or biological relationships between the datasets. DPM prioritises genes and pathways that change consistently across the datasets and penalises those with inconsistent directionality. To demonstrate our approach, we characterise gene and pathway regulation in IDH-mutant gliomas by jointly analysing transcriptomic, proteomic, and DNA methylation datasets. Directional integration of survival information in ovarian cancer reveals candidate biomarkers with consistent prognostic signals in transcript and protein expression. DPM is a general and adaptable framework for gene prioritisation and pathway analysis in multi-omics datasets.
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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.