ArticleNucleic acids research2020
NetCore: a network propagation approach using node coreness.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs.Communications biology · 2026Article
- RNA stability: a novel perspective on gene regulatory networks in bovine mastitis.BMC genomics · 2025Article
- A new Similarity Based Adapted Louvain Algorithm (SIMBA) for active module identification in p-value attributed biological networks.Scientific reports · 2025Article
- Temporal phosphoproteomics reveals circuitry of phased propagation in insulin signaling.Nature communications · 2025Article
- AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs.BMC bioinformatics · 2025Article
- A comprehensive benchmark study of methods for identifying significantly perturbed subnetworks in cancer.Briefings in bioinformatics · 2024Article
- Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks.Bioinformatics (Oxford, England) · 2024Article
- Network propagation for GWAS analysis: a practical guide to leveraging molecular networks for disease gene discovery.Briefings in bioinformatics · 2024Review
- Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation.BMC bioinformatics · 2024Article
- AMEND: active module identification using experimental data and network diffusion.BMC bioinformatics · 2023Article
- Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers.Nucleic acids research · 2023Article
- Atlas of interactions between SARS-CoV-2 macromolecules and host proteins.Cell insight · 2023Article
- Host M-CSF induced gene expression drives changes in susceptible and resistant mice-derived BMdMs uponFrontiers in immunology · 2023Article
- Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Network-Based Approaches for Disease-Gene Association Prediction Using Protein-Protein Interaction Networks.International journal of molecular sciences · 2022Article
- Gradient tree boosting and network propagation for the identification of pan-cancer survival networks.STAR protocols · 2022Article
- Molecular Subgroup Classification in Alzheimer's Disease by Transcriptomic Profiles.Journal of molecular neuroscience : MN · 2022Article
- A gradient tree boosting and network propagation derived pan-cancer survival network of the tumor microenvironment.iScience · 2022Article
- ConsensusPathDB 2022: molecular interactions update as a resource for network biology.Nucleic acids research · 2022Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present NetCore, a novel network propagation approach based on node coreness, for phenotype-genotype associations and module identification. NetCore addresses the node degree bias in PPI networks by using node coreness in the random walk with restart procedure, and achieves improved re-ranking of genes after propagation. Furthermore, NetCore implements a semi-supervised approach to identify phenotype-associated network modules, which anchors the identification of novel candidate genes at known genes associated with the phenotype. We evaluated NetCore on gene sets from 11 different GWAS traits and showed improved performance compared to the standard degree-based network propagation using cross-validation. Furthermore, we applied NetCore to identify disease genes and modules for Schizophrenia GWAS data and pan-cancer mutation data. We compared the novel approach to existing network propagation approaches and showed the benefits of using NetCore in comparison to those. We provide an easy-to-use implementation, together with a high confidence PPI network extracted from ConsensusPathDB, which can be applied to various types of genomics data in order to obtain a re-ranking of genes and functionally relevant network modules.
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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.