ArticleCell research2012
A network-based gene-weighting approach for pathway analysis.
Article in Cell research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- MetaScreener: a robust dual-mode framework for directional prioritization of actionable signatures through multi-dataset and multi-approach integration.Journal of translational medicine · 2026Article
- Rethinking network analysis in ethnopharmacology: a multi-omics and AI roadmap to overcome conceptual and methodological biases.Frontiers in pharmacology · 2026Article
- GNNenrich: a novel method for pathway enrichment analysis based on graph neural network.Bioinformatics (Oxford, England) · 2025Article
- Longitudinal pathway analysis using structural information with case studies in early type 1 diabetes.Scientific reports · 2025Article
- ActivePPI: quantifying protein-protein interaction network activity with Markov random fields.Bioinformatics (Oxford, England) · 2023Article
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- KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis.Nucleic acids research · 2021Article
- Article
- Gene-set Enrichment with Mathematical Biology (GEMB).GigaScience · 2020Article
- Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations.Genome biology · 2020Article
- Identification of Long Noncoding RNA Biomarkers for Hepatocellular Carcinoma Using Single-Sample Networks.BioMed research international · 2020Article
- A network-based pathway-extending approach using DNA methylation and gene expression data to identify altered pathways.Scientific reports · 2019Article
- Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.Nature protocols · 2019Article
- SCIA: A Novel Gene Set Analysis Applicable to Data With Different Characteristics.Frontiers in genetics · 2019Article
- Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis.BMC genomics · 2018Article
- The microRNA-182-PDK4 axis regulates lung tumorigenesis by modulating pyruvate dehydrogenase and lipogenesis.Oncogene · 2017Article
- A network-based pathway-expanding approach for pathway analysis.BMC bioinformatics · 2016Article
- Personalized characterization of diseases using sample-specific networks.Nucleic acids research · 2016Article
- Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways.Scientific reports · 2016Article
- LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights.Scientific reports · 2016Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Classical algorithms aiming at identifying biological pathways significantly related to studying conditions frequently reduced pathways to gene sets, with an obvious ignorance of the constitutive non-equivalence of various genes within a defined pathway. We here designed a network-based method to determine such non-equivalence in terms of gene weights. The gene weights determined are biologically consistent and robust to network perturbations. By integrating the gene weights into the classical gene set analysis, with a subsequent correction for the "over-counting" bias associated with multi-subunit proteins, we have developed a novel gene-weighed pathway analysis approach, as implemented in an R package called "Gene Associaqtion Network-based Pathway Analysis" (GANPA). Through analysis of several microarray datasets, including the p53 dataset, asthma dataset and three breast cancer datasets, we demonstrated that our approach is biologically reliable and reproducible, and therefore helpful for microarray data interpretation and hypothesis generation.
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