ArticleBMC bioinformatics2024
vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis.
Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Cross-Species and Sex-Specific Meta-Analysis of Transcriptomic Studies of Pulmonary Hypertension.American journal of respiratory cell and molecular biology · 2025Pooled it
- OXR1 is a dual redox-mitochondrial checkpoint governing osteoclast differentiation and bone loss in an osteoporosis mouse model.Nature communications · 2026Article
- hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- Multi-omics investigation of thyroid development and dysfunction in down syndrome.Human molecular genetics · 2026Article
- Cancer cell-intrinsic inflammasome protein ASC links innate immunity with mitochondrial metabolism in driving pancreatic cancer.Nature communications · 2026Article
- Divergent cytokine and transcriptional signatures control functional T follicular helper cell heterogeneity.Nature immunology · 2025Article
- GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis.BMC bioinformatics · 2025Article
- Pathway Analysis Interpretation in the Multi-Omic Era.Biotech (Basel (Switzerland)) · 2025Review
- Extrachromosomal circular DNAs in the differentiation of human bone marrow mesenchymal stem cells.Stem cell research & therapy · 2025Article
- Extracellular vesicle-associated miR-515-5p from adipose tissue regulates placental metabolism and fetal growth in gestational diabetes mellitus.Cardiovascular diabetology · 2025Article
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- biotextgraph: graphical summarization of functional similarities from textual information.Bioinformatics (Oxford, England) · 2024Article
- Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies placental dysfunction signatures.Clinical & translational immunology · 2024Article
- vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis.Nucleic acids research · 2023Article
- Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage.Immunology · 2023Article
Corrections and comments
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Authors and funding
9 authors.
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Abstract
Functional analysis of high throughput experiments using pathway analysis is now ubiquitous. Though powerful, these methods often produce thousands of redundant results owing to knowledgebase redundancies upstream. This scale of results hinders extensive exploration by biologists and can lead to investigator biases due to previous knowledge and expectations. To address this issue, we present vissE, a flexible network-based analysis and visualisation tool that organises information into semantic categories and provides various visualisation modules to characterise them with respect to the underlying data, thus providing a comprehensive view of the biological system. We demonstrate vissE's versatility by applying it to three different technologies: bulk, single-cell and spatial transcriptomics. Applying vissE to a factor analysis of a breast cancer spatial transcriptomic data, we identified stromal phenotypes that support tumour dissemination. Its adaptability allows vissE to enhance all existing gene-set enrichment and pathway analysis workflows, empowering biologists during molecular discovery.
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