ArticlePLoS computational biology2024
PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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
18 citing papers in PubMed.
- Biochemically Constrained Multi-Omics Integration Reveals Protein-Metabolite Dependencies Across Diseases.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- iDCF: Interpretable deconvolution of cell fractions via biologically-informed deep learning using scRNA-seq data.PLoS computational biology · 2026Article
- Network-based integration of metabolomics data from large-scale repositories.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Longitudinal urine metabolomics predicts high-grade brain injury in very preterm infants.Pediatric research · 2026Article
- Research progress on the Sonic Hedgehog signaling pathway in the central nervous system: Novel insights.Neural regeneration research · 2026Article
- A lipidomics roadmap: from basic research to societal challenges.Nature communications · 2026Review
- The crosstalk between epigenetics and metabolism in the malignant cell.Discover oncology · 2026Review
- Article
- The multi-omic basis for hepatic encephalopathy recurrence: Analysis of the THEMATIC trial.JHEP reports : innovation in hepatology · 2026Article
- 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
- MAMSI: Integration of Multiassay Liquid Chromatography-Mass Spectrometry Metabolomics Data Using Multiview Machine Learning.Analytical chemistry · 2025Article
- Phoenics: a novel statistical approach for longitudinal metabolomic pathway analysis.BMC bioinformatics · 2025Article
- Pathway level metabolomics analysis identifies carbon metabolism as a key factor of incident hypertension in the Estonian Biobank.Scientific reports · 2025Article
- Omics Approaches in Understanding Insecticide Resistance in Mosquito Vectors.International journal of molecular sciences · 2025Review
- PathX-CNN: An Enhanced Explainable Convolutional Neural Network for Survival Prediction and Pathway Analysis in Glioblastoma.bioRxiv : the preprint server for biology · 2025Article
- Synthetic data generation methods in healthcare: A review on open-source tools and methods.Computational and structural biotechnology journal · 2024Review
- Deciphering the molecular heterogeneity of intermediate- and (very-)high-risk non-muscle-invasive bladder cancer using multi-layeredFrontiers in oncology · 2024Article
Corrections and comments
- Update of
Authors and funding
9 authors.
Funding
Abstract
As terabytes of multi-omics data are being generated, there is an ever-increasing need for methods facilitating the integration and interpretation of such data. Current multi-omics integration methods typically output lists, clusters, or subnetworks of molecules related to an outcome. Even with expert domain knowledge, discerning the biological processes involved is a time-consuming activity. Here we propose PathIntegrate, a method for integrating multi-omics datasets based on pathways, designed to exploit knowledge of biological systems and thus provide interpretable models for such studies. PathIntegrate employs single-sample pathway analysis to transform multi-omics datasets from the molecular to the pathway-level, and applies a predictive single-view or multi-view model to integrate the data. Model outputs include multi-omics pathways ranked by their contribution to the outcome prediction, the contribution of each omics layer, and the importance of each molecule in a pathway. Using semi-synthetic data we demonstrate the benefit of grouping molecules into pathways to detect signals in low signal-to-noise scenarios, as well as the ability of PathIntegrate to precisely identify important pathways at low effect sizes. Finally, using COPD and COVID-19 data we showcase how PathIntegrate enables convenient integration and interpretation of complex high-dimensional multi-omics datasets. PathIntegrate is available as an open-source Python package.
Indexed as
Identifiers
What Socratic 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 Socratic graph.