ArticlePloS one2015
Subpathway Analysis based on Signaling-Pathway Impact Analysis of Signaling Pathway.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 51 citations in OpenAlex.
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- A drug repurposing method based on inhibition effect on gene regulatory network.Computational and structural biotechnology journal · 2023Article
- Identification of altered miRNAs and their targets in placenta accreta.Frontiers in endocrinology · 2023Article
- Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.Molecular systems biology · 2022Review
- Treatment of HT29 Human Colorectal Cancer Cell Line with Nanocarrier-Encapsulated Camptothecin Reveals Histone Modifier Genes in theInternational journal of molecular sciences · 2021Article
- Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data.Computational and structural biotechnology journal · 2021Article
- Identifying disease-associated signaling pathways through a novel effector gene analysis.PeerJ · 2020Article
- Pathway Maps of Orphan and Complex Diseases Using an Integrative Computational Approach.BioMed research international · 2020Article
- SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways.PLoS computational biology · 2019Article
- A comparison of mechanistic signaling pathway activity analysis methods.Briefings in bioinformatics · 2019Review
- The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database.BMC bioinformatics · 2019Article
- Sub-pathway based approach to systematically track candidate sub-pathway biomarkers for heart failure.Experimental and therapeutic medicine · 2019Article
- Differential effects, on oncogenic pathway signalling, by derivatives of the HNF4 α inhibitor BI6015.British journal of cancer · 2019Article
- Identifying cancer-related microRNAs based on subpathways.IET systems biology · 2018Article
- Pathway networks generated from human disease phenome.BMC medical genomics · 2018Article
- sPAGM: inferring subpathway activity by integrating gene and miRNA expression-robust functional signature identification for melanoma prognoses.Scientific reports · 2017Article
- High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.Oncotarget · 2017Article
- Null diffusion-based enrichment for metabolomics data.PloS one · 2017Article
- Signalling pathway impact analysis based on the strength of interaction between genes.IET systems biology · 2016Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pathway analysis is a common approach to gain insight from biological experiments. Signaling-pathway impact analysis (SPIA) is one such method and combines both the classical enrichment analysis and the actual perturbation on a given pathway. Because this method focuses on a single pathway, its resolution generally is not very high because the differentially expressed genes may be enriched in a local region of the pathway. In the present work, to identify cancer-related pathways, we incorporated a recent subpathway analysis method into the SPIA method to form the "sub-SPIA method." The original subpathway analysis uses the k-clique structure to define a subpathway. However, it is not sufficiently flexible to capture subpathways with complex structure and usually results in many overlapping subpathways. We therefore propose using the minimal-spanning-tree structure to find a subpathway. We apply this approach to colorectal cancer and lung cancer datasets, and our results show that sub-SPIA can identify many significant pathways associated with each specific cancer that other methods miss. Based on the entire pathway network in the Kyoto Encyclopedia of Genes and Genomes, we find that the pathways identified by sub-SPIA not only have the largest average degree, but also are more closely connected than those identified by other methods. This result suggests that the abnormality signal propagating through them might be responsible for the specific cancer or disease.
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