ArticleNucleic acids research2023
Integration of gene expression and DNA methylation data across different experiments.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
- Epigenetic biomarkers in inflammatory bowel diseases-computational challenges and opportunities.Journal of Crohn's & colitis · 2026Review
- Artificial Intelligence Design for Race-Based Prostate Cancer Stage Classification With Multilayer Perceptron: Feature Selection Optimization Approach.JMIR formative research · 2026Article
- Deep capsule neural network for identifying anticancer peptides using sequence to image transformation-based local embedded features.BMC biology · 2026Article
- Early microglial priming in Alzheimer's disease revealed by ME-seq.bioRxiv : the preprint server for biology · 2026Article
- MCLCBA: multi-view contrastive learning network for RNA methylation site prediction.BMC bioinformatics · 2025Article
- Coordinated Transcriptomic and Epigenetic Approach Reveals Molecular Features Underlying Natural Mating Ability in Captive Male Giant Pandas.Ecology and evolution · 2025Article
- PRMT5 regulates alternative splicing of TCF3 under hypoxia to promote EMT and invasion in breast cancer.PLoS biology · 2025Article
- Hybridization and gene expression: Beyond differentially expressed genes.Molecular ecology · 2025Review
- Detection of an intestinal cell DNA methylation signature in blood samples from neonates with necrotizing enterocolitis.Epigenomics · 2025Article
- IL-1β and associated molecules as prognostic biomarkers linked with immune cell infiltration in colorectal cancer: an integrated statistical and machine learning approach.Discover oncology · 2025Article
- Acetylation-Mediated Epigenetic Consequences for Biological Control and Cancer.Results and problems in cell differentiation · 2025Review
- Article
- The amino acid transporter SLC7A11 expression in breast cancer.Cancer biology & therapy · 2024Article
- scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features.Nature communications · 2024Article
- Genome-wide DNA methylation profiles and breast cancer among World Trade Center survivors.Environmental epidemiology (Philadelphia, Pa.) · 2024Article
- Epigenetic modulation of myeloid cell functions in HIV and SARS-CoV-2 infection.Molecular biology reports · 2024Review
- Clinical role of NDRG2-based methylation status on survival pattern of glioblastoma.International journal of immunopathology and pharmacologyArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integrative analysis of multi-omic datasets has proven to be extremely valuable in cancer research and precision medicine. However, obtaining multimodal data from the same samples is often difficult. Integrating multiple datasets of different omics remains a challenge, with only a few available algorithms developed to solve it. Here, we present INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples. To enable integration, INTEND learns a predictive model between the two omics by training on multi-omic data measured on the same set of samples. In comprehensive testing on 11 TCGA (The Cancer Genome Atlas) cancer datasets spanning 4329 patients, INTEND achieves significantly superior results compared with four state-of-the-art integration algorithms. We also demonstrate INTEND's ability to uncover connections between DNA methylation and the regulation of gene expression in the joint analysis of two lung adenocarcinoma single-omic datasets from different sources. INTEND's data-driven approach makes it a valuable multi-omic data integration tool. The code for INTEND is available at https://github.com/Shamir-Lab/INTEND.
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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.