ArticleScientific reports2015
ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Molecular Networks and Key Regulators Underlying Resilience of the Human Brain to Aging and Dementia.Biomolecules · 2026Article
- PLNFGL: joint estimation of multi-condition gene networks from single-cell RNA-seq data.Bioinformatics (Oxford, England) · 2026Article
- scRDEN: single-cell dynamic gene rank differential expression network and robust trajectory inference.Scientific reports · 2025Article
- A Network Toxicology Approach for Mechanistic Modelling of Nanomaterial Hazard and Adverse Outcomes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Patient-specific analysis of co-expression to measure biological network rewiring in individuals.Life science alliance · 2024Article
- Improving the performance of single-cell RNA-seq data mining based on relative expression orderings.Briefings in bioinformatics · 2023Article
- LncSEA: a platform for long non-coding RNA related sets and enrichment analysis.Nucleic acids research · 2021Article
- DysPIA: A Novel Dysregulated Pathway Identification Analysis Method.Frontiers in genetics · 2021Article
- Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression.International journal of molecular sciences · 2020Review
- IP4M: an integrated platform for mass spectrometry-based metabolomics data mining.BMC bioinformatics · 2020Article
- Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity?Biomolecules · 2020Article
- A framework using topological pathways for deeper analysis of transcriptome data.BMC genomics · 2020Article
- Inference of Subpathway Activity Profiles Reveals Metabolism Abnormal Subpathway Regions in Glioblastoma Multiforme.Frontiers in oncology · 2020Article
- SCIA: A Novel Gene Set Analysis Applicable to Data With Different Characteristics.Frontiers in genetics · 2019Article
- Article
- DynSig: Modelling Dynamic Signaling Alterations along Gene Pathways for Identifying Differential Pathways.Genes · 2018Article
- Model-based analysis of competing-endogenous pathways (MACPath) in human cancers.PLoS computational biology · 2018Article
- Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare.BMC systems biology · 2017Article
- Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways.Scientific reports · 2017Article
- Bayesian model of signal rewiring reveals mechanisms of gene dysregulation in acquired drug resistance in breast cancer.PloS one · 2017Article
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13 authors.
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Abstract
Pathway analyses are playing an increasingly important role in understanding biological mechanism, cellular function and disease states. Current pathway-identification methods generally focus on only the changes of gene expression levels; however, the biological relationships among genes are also the fundamental components of pathways, and the dysregulated relationships may also alter the pathway activities. We propose a powerful computational method, Edge Set Enrichment Analysis (ESEA), for the identification of dysregulated pathways. This provides a novel way of pathway analysis by investigating the changes of biological relationships of pathways in the context of gene expression data. Simulation studies illustrate the power and performance of ESEA under various simulated conditions. Using real datasets from p53 mutation, Type 2 diabetes and lung cancer, we validate effectiveness of ESEA in identifying dysregulated pathways. We further compare our results with five other pathway enrichment analysis methods. With these analyses, we show that ESEA is able to help uncover dysregulated biological pathways underlying complex traits and human diseases via specific use of the dysregulated biological relationships. We develop a freely available R-based tool of ESEA. Currently, ESEA can support pathway analysis of the seven public databases (KEGG; Reactome; Biocarta; NCI; SPIKE; HumanCyc; Panther).
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