ArticleBMC genomics2015
A computational framework for the prioritization of disease-gene candidates.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Integrative bioinformatics frameworks for abdominal aortic aneurysm using GWAS meta-analysis, biological network construction, and structural modeling.Scientific reports · 2025Pooled it
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- Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content.Horticulture research · 2024Article
- Transcriptional Regulation of SugarCane Response toJournal of agricultural and food chemistry · 2024Article
- Cytogenomic epileptology.Molecular cytogenetics · 2023Review
- Understanding mental health through computers: An introduction to computational psychiatry.Frontiers in psychiatry · 2023Review
- Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color.Horticulture research · 2023Article
- GediNET for discovering gene associations across diseases using knowledge based machine learning approach.Scientific reports · 2022Article
- Integrated co-expression network analysis uncovers novel tissue-specific genes in major depressive disorder and bipolar disorder.Frontiers in psychiatry · 2022Article
- A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer's Disease.Frontiers in neuroscience · 2020Article
- A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases.Journal of integrative bioinformatics · 2019Review
- Network-based integrated analysis of omics data reveal novel players of TGF-β1-induced EMT in human peritoneal mesothelial cells.Scientific reports · 2019Article
- Re-thinking Alzheimer's disease therapeutic targets using gene-based tests.EBioMedicine · 2018Article
- Predicting disease-related genes using integrated biomedical networks.BMC genomics · 2017Article
- Mining the literature for genes associated with placenta-mediated maternal diseases.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe identification of genes and uncovering the role they play in diseases is an important and complex challenge. Genome-wide linkage and association studies have made advancements in identifying genetic variants that underpin human disease. An important challenge now is to identify meaningful disease-associated genes from a long list of candidate genes implicated by these analyses. The application of gene prioritization can enhance our understanding of disease mechanisms and aid in the discovery of drug targets. The integration of protein-protein interaction networks along with disease datasets and contextual information is an important tool in unraveling the molecular basis of diseases.
resultsIn this paper we propose a computational pipeline for the prioritization of disease-gene candidates. Diverse heterogeneous data including: gene-expression, protein-protein interaction network, ontology-based similarity and topological measures and tissue-specific are integrated. The pipeline was applied to prioritize Alzheimer's Disease (AD) genes, whereby a list of 32 prioritized genes was generated. This approach correctly identified key AD susceptible genes: PSEN1 and TRAF1. Biological process enrichment analysis revealed the prioritized genes are modulated in AD pathogenesis including: regulation of neurogenesis and generation of neurons. Relatively high predictive performance (AUC: 0.70) was observed when classifying AD and normal gene expression profiles from individuals using leave-one-out cross validation.
conclusionsThis work provides a foundation for future investigation of diverse heterogeneous data integration for disease-gene prioritization.
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