ArticleScientific reports2020
Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance.
Article in Scientific reports, 2020. 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.
- thematicGO: A Keyword-Based Framework for Interpreting Gene Ontology Enrichment via Biological Themes.bioRxiv : the preprint server for biology · 2026Article
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- Generation of 12Computational and structural biotechnology journal · 2025Article
- Optimizing gene selection and module identification via ontology-based scoring and deep learning.Bioinformatics advances · 2025Article
- Beyond the Nucleus: Plastic Chemicals Activate G Protein-Coupled Receptors.Environmental science & technology · 2024Article
- A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora.BMC biology · 2024Article
- Transcriptomic Analyses of Neurotoxic Astrocytes Derived from Adult Triple Transgenic Alzheimer's Disease Mice.Journal of molecular neuroscience : MN · 2023Article
- Parallel and convergent genomic changes underlie independent subterranean colonization across beetles.Nature communications · 2023Article
- The Foundational Data Initiative for Parkinson Disease: Enabling efficient translation from genetic maps to mechanism.Cell genomics · 2023Article
- Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery.NPJ systems biology and applications · 2022Article
- EventPointer 3.0: flexible and accurate splicing analysis that includes studying the differential usage of protein-domains.NAR genomics and bioinformatics · 2022Article
- RNA sequencing of whole blood reveals early alterations in immune cells and gene expression in Parkinson's disease.Nature aging · 2021Article
- Prognostic gene expression signatures of breast cancer are lacking a sensible biological meaning.Scientific reports · 2021Article
- Testing biological network motif significance with exponential random graph models.Applied network science · 2021Article
- Limitations of Explainability for Established Prognostic Biomarkers of Prostate Cancer.Frontiers in genetics · 2021Article
- Data-Driven Computational Social Network Science: Predictive and Inferential Models for Web-Enabled Scientific Discoveries.Frontiers in big data · 2021Article
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5 authors.
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Abstract
Gene ontology (GO) is an eminent knowledge base frequently used for providing biological interpretations for the analysis of genes or gene sets from biological, medical and clinical problems. Unfortunately, the interpretation of such results is challenging due to the large number of GO terms, their hierarchical and connected organization as directed acyclic graphs (DAGs) and the lack of tools allowing to exploit this structural information explicitly. For this reason, we developed the R package GOxploreR. The main features of GOxploreR are (I) easy and direct access to structural features of GO, (II) structure-based ranking of GO-terms, (III) mapping to reduced GO-DAGs including visualization capabilities and (IV) prioritizing of GO-terms. The underlying idea of GOxploreR is to exploit a graph-theoretical perspective of GO as manifested by its DAG-structure and the containing hierarchy levels for cumulating semantic information. That means all these features enhance the utilization of structural information of GO and complement existing analysis tools. Overall, GOxploreR provides exploratory as well as confirmatory tools for complementing any kind of analysis resulting in a list of GO-terms, e.g., from differentially expressed genes or gene sets, GWAS or biomarkers. Our R package GOxploreR is freely available from CRAN.
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