ArticleBMC systems biology2018
Identification of active signaling pathways by integrating gene expression and protein interaction data.
Article in BMC systems biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- The Genus Paeonia: A Review of the Targeted Signaling Pathways and Underlying Mechanisms of Pharmacological and Clinical Properties.Current drug discovery technologies · 2025Review
- Whole-genome sequencing shows modulation of neurodegenerative genes byFrontiers in molecular neuroscience · 2025Article
- Signaling pathways of dental implants' osseointegration: a narrative review on two of the most relevant; NF-κB and Wnt pathways.BDJ open · 2024Review
- PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during development.Life science alliance · 2024Article
- Using epigenomics to understand cellular responses to environmental influences in diseases.PLoS genetics · 2023Review
- Signaling network analysis reveals fostamatinib as a potential drug to control platelet hyperactivation during SARS-CoV-2 infection.Frontiers in immunology · 2023Article
- Transcriptomic Responses of Human Retinal Vascular Endothelial Cells to Inflammatory Cytokines.Translational vision science & technology · 2022Article
- Nanotechnology Approaches for Enhanced CNS Drug Delivery in the Management of Schizophrenia.Advanced pharmaceutical bulletin · 2022Review
- Signaling Pathways Involved in Myocardial Ischemia-Reperfusion Injury and Cardioprotection: A Systematic Review of Transcriptomic Studies inJournal of cardiovascular development and disease · 2022Review
- Review
- Efficient induction and sustenance of pluripotent stem cells from bovine somatic cells.Biology open · 2021Article
- Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells.Science advances · 2021Article
- Vertical integration methods for gene expression data analysis.Briefings in bioinformatics · 2021Review
- Single cell RNA-sequencing data generated from human pluripotent stem cell-derived lens epithelial cells.Data in brief · 2021Article
- Application of the RBBP9 Serine Hydrolase Inhibitor, ML114, Decouples Human Pluripotent Stem Cell Proliferation and Differentiation.International journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSignaling pathways are the key biological mechanisms that transduce extracellular signals to affect transcription factor mediated gene regulation within cells. A number of computational methods have been developed to identify the topological structure of a specific signaling pathway using protein-protein interaction data, but they are not designed for identifying active signaling pathways in an unbiased manner. On the other hand, there are statistical methods based on gene sets or pathway data that can prioritize likely active signaling pathways, but they do not make full use of active pathway structure that link receptor, kinases and downstream transcription factors.
resultsHere, we present a method to simultaneously predict the set of active signaling pathways, together with their pathway structure, by integrating protein-protein interaction network and gene expression data. We evaluated the capacity for our method to predict active signaling pathways for dental epithelial cells, ocular lens epithelial cells, human pluripotent stem cell-derived lens epithelial cells, and lens fiber cells. This analysis showed our approach could identify all the known active pathways that are associated with tooth formation and lens development.
conclusionsThe results suggest that SPAGI can be a useful approach to identify the potential active signaling pathways given a gene expression profile. Our method is implemented as an open source R package, available via https://github.com/VCCRI/SPAGI/ .
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