ArticleNucleic acids research2013
TEAK: topology enrichment analysis framework for detecting activated biological subpathways.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.Molecular systems biology · 2022Review
- MiRNA-Mediated Subpathway Identification and Network Module Analysis to Reveal Prognostic Markers in Human Pancreatic Cancer.Frontiers in genetics · 2020Article
- Topologically inferring active miRNA-mediated subpathways toward precise cancer classification by directed random walk.Molecular oncology · 2019Article
- A comparison of mechanistic signaling pathway activity analysis methods.Briefings in bioinformatics · 2019Review
- FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods.BMC bioinformatics · 2019Article
- Investigating the aetiology of adverse events following HPV vaccination with systems vaccinology.Cellular and molecular life sciences : CMLS · 2019Review
- Identification of Cancer Dysfunctional Subpathways by Integrating DNA Methylation, Copy Number Variation, and Gene-Expression Data.Frontiers in genetics · 2019Article
- Identification of Common and Subtype-Specific Mutated Sub-Pathways for a Cancer.Frontiers in genetics · 2019Article
- Expression of Nestin associates with BRCA1 mutations, a basal-like phenotype and aggressive breast cancer.Scientific reports · 2017Article
- Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach.Non-coding RNA · 2017Article
- High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.Oncotarget · 2017Article
- MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways.PLoS computational biology · 2016Article
- Cofunctional Subpathways Were Regulated by Transcription Factor with Common Motif, Common Family, or Common Tissue.BioMed research international · 2015Article
- Understanding disease mechanisms with models of signaling pathway activities.BMC systems biology · 2014Article
- Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae.BMC systems biology · 2014Article
- Revealing Biological Pathways Implicated in Lung Cancer from TCGA Gene Expression Data Using Gene Set Enrichment Analysis.Cancer informatics · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
To mine gene expression data sets effectively, analysis frameworks need to incorporate methods that identify intergenic relationships within enriched biologically relevant subpathways. For this purpose, we developed the Topology Enrichment Analysis frameworK (TEAK). TEAK employs a novel in-house algorithm and a tailor-made Clique Percolation Method to extract linear and nonlinear KEGG subpathways, respectively. TEAK scores subpathways using the Bayesian Information Criterion for context specific data and the Kullback-Leibler divergence for case-control data. In this article, we utilized TEAK with experimental studies to analyze microarray data sets profiling stress responses in the model eukaryote Saccharomyces cerevisiae. Using a public microarray data set, we identified via TEAK linear sphingolipid metabolic subpathways activated during the yeast response to nitrogen stress, and phenotypic analyses of the corresponding deletion strains indicated previously unreported fitness defects for the dpl1Δ and lag1Δ mutants under conditions of nitrogen limitation. In addition, we studied the yeast filamentous response to nitrogen stress by profiling changes in transcript levels upon deletion of two key filamentous growth transcription factors, FLO8 and MSS11. Via TEAK we identified a nonlinear glycerophospholipid metabolism subpathway involving the SLC1 gene, which we found via mutational analysis to be required for yeast filamentous growth.
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