ArticleFrontiers in genetics2019
Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome.
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- AI-enabled drug prediction and gene network analysis reveal therapeutic use of vorinostat for Rett Syndrome in preclinical models.Communications medicine · 2025Article
- RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape.Database : the journal of biological databases and curation · 2024Article
- Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions.PloS one · 2022Article
- A resource to explore the discovery of rare diseases and their causative genes.Scientific data · 2021Article
- Multi-omics: Differential expression of IFN-γ results in distinctive mechanistic features linking chronic inflammation, gut dysbiosis, and autoimmune diseases.Journal of autoimmunity · 2020Article
- The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling.Frontiers in genetics · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pathway and network approaches are valuable tools in analysis and interpretation of large complex omics data. Even in the field of rare diseases, like Rett syndrome, omics data are available, and the maximum use of such data requires sophisticated tools for comprehensive analysis and visualization of the results. Pathway analysis with differential gene expression data has proven to be extremely successful in identifying affected processes in disease conditions. In this type of analysis, pathways from different databases like WikiPathways and Reactome are used as separate, independent entities. Here, we show for the first time how these pathway models can be used and integrated into one large network using the WikiPathways RDF containing all human WikiPathways and Reactome pathways, to perform network analysis on transcriptomics data. This network was imported into the network analysis tool Cytoscape to perform active submodule analysis. Using a publicly available Rett syndrome gene expression dataset from frontal and temporal cortex, classical enrichment analysis, including pathway and Gene Ontology analysis, revealed mainly immune response, neuron specific and extracellular matrix processes. Our active module analysis provided a valuable extension of the analysis prominently showing the regulatory mechanism of
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Registered trials
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