ArticleiScience2019
A Fast and Flexible Framework for Network-Assisted Genomic Association.
Article in iScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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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Who cites it
16 citing papers in PubMed, 33 citations in OpenAlex.
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- Current and future directions in network biology.Bioinformatics advances · 2024Article
- Lithium Response in Bipolar Disorder is Associated with Focal Adhesion and PI3K-Akt Networks: A Multi-omics Replication Study.Research square · 2023Article
- Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks.Cell reports · 2023Article
- networkGWAS: a network-based approach to discover genetic associations.Bioinformatics (Oxford, England) · 2023Article
- Self-supervised graph representation learning integrates multiple molecular networks and decodes gene-disease relationships.Patterns (New York, N.Y.) · 2023Article
- NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Genetically personalised organ-specific metabolic models in health and disease.Nature communications · 2022Article
- Multiscale modeling in the framework of biological systems and its potential for spaceflight biology studies.iScience · 2022Review
- mGWAS-Explorer: Linking SNPs, Genes, Metabolites, and Diseases for Functional Insights.Metabolites · 2022Article
- Network and pathway expansion of genetic disease associations identifies successful drug targets.Scientific reports · 2020Article
- NetCore: a network propagation approach using node coreness.Nucleic acids research · 2020Article
- uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes.Cell systems · 2020Article
- FI-Net: Identification of Cancer Driver Genes by Using Functional Impact Prediction Neural Network.Frontiers in genetics · 2020Article
- Strategies for Network GWAS Evaluated Using Classroom Crowd Science.Cell systems · 2019Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
We present an accessible, fast, and customizable network propagation system for pathway boosting and interpretation of genome-wide association studies. This system-NAGA (Network Assisted Genomic Association)-taps the NDEx biological network resource to gain access to thousands of protein networks and select those most relevant and performative for a specific association study. The method works efficiently, completing genome-wide analysis in under 5 minutes on a modern laptop computer. We show that NAGA recovers many known disease genes from analysis of schizophrenia genetic data, and it substantially boosts associations with previously unappreciated genes such as amyloid beta precursor. On this and seven other gene-disease association tasks, NAGA outperforms conventional approaches in recovery of known disease genes and replicability of results. Protein interactions associated with disease are visualized and annotated in Cytoscape, which, in addition to standard programmatic interfaces, allows for downstream analysis.
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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.