ArticleMammalian genome : official journal of the International Mammalian Genome Society2015
Visual annotation display (VLAD): a tool for finding functional themes in lists of genes.
Article in Mammalian genome : official journal of the International Mammalian Genome Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- Svep1 orchestrates distal airway patterning and alveolar differentiation in murine lung development.eLife · 2026Article
- Maternal Inflammation Alters Nuclear and Mitochondrial DNA Methylation Patterns in Neonatal Brain Monocytes.Cells · 2026Article
- Sex and Genotype Affect Mouse Hippocampal Gene Expression in Response to Blast-Induced Traumatic Brain Injury.Molecular neurobiology · 2025Article
- Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional-Post-Transcriptional Regulatory Cross-Talk.Biology · 2025Article
- Effective knockdown-replace gene therapy in a novel mouse model of DNM1 developmental and epileptic encephalopathy.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
- GOTermViewer: Visualization of Gene Ontology Enrichment in Multiple Differential Gene Expression Analyses.Bioinformatics and biology insights · 2024Article
- Article
- Transcriptomic analysis reveals the role of SIX1 in mouse cranial neural crest patterning and bone development.Developmental dynamics : an official publication of the American Association of Anatomists · 2023Article
- Biochemical Pathways Represented by Gene Ontology Causal Activity Models Identify Distinct Phenotypes Resulting from Mutations in Pathways.bioRxiv : the preprint server for biology · 2023Article
- Diet suppresses glioblastoma initiation in mice by maintaining quiescence of mutation-bearing neural stem cells.Developmental cell · 2023Article
- GOing Forward With the Cardiac Conduction System Using Gene Ontology.Frontiers in genetics · 2022Article
- Cigarette Smoke Triggers Loss of Corneal Endothelial Cells and Disruption of Descemet's Membrane Proteins in Mice.Investigative ophthalmology & visual science · 2021Article
- Transcriptome Analysis Identifies SenZfp536, a Sense LncRNA that Suppresses Self-renewal of Cortical Neural Progenitors.Neuroscience bulletin · 2021Article
- Selective sweep analysis reveals extensive parallel selection traits between large white and Duroc pigs.Evolutionary applications · 2020Article
- Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease.Scientific reports · 2020Article
- Prenatal Androgenization Alters the Development of GnRH Neuron and Preoptic Area RNA Transcripts in Female Mice.Endocrinology · 2020Article
- Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease.bioRxiv : the preprint server for biology · 2020Article
- Exploring mechanisms of increased cardiovascular disease risk with antipsychotic medications: Risperidone alters the cardiac proteomic signature in mice.Pharmacological research · 2020Article
- Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data.Journal of Alzheimer's disease : JAD · 2020Article
- Effects of a male meiotic driver on male and female transcriptomes in the house mouse.Proceedings. Biological sciences · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Experiments that employ genome scale technology platforms frequently result in lists of tens to thousands of genes with potential significance to a specific biological process or disease. Searching for biologically relevant connections among the genes or gene products in these lists is a common data analysis task. We have implemented a software application for uncovering functional themes in sets of genes based on their annotations to bio-ontologies, such as the gene ontology and the mammalian phenotype ontology. The application, called VisuaL Annotation Display (VLAD), performs a statistical analysis to test for the enrichment of ontology terms in a set of genes submitted by a researcher. The results for each analysis using VLAD includes a table of ontology terms, sorted in decreasing order of significance. Each row contains the term, statistics such as the number of annotated terms, the p value, etc., and the symbols of annotated genes. An accompanying graphical display shows portions of the ontology hierarchy, where node sizes are scaled based on p values. Although numerous ontology term enrichment programs already exist, VLAD is unique in that it allows users to upload their own annotation files and ontologies for customized term enrichment analyses, supports the analysis of multiple gene sets at once, provides interfaces to customize graphical output, and is tightly integrated with functional and biological details about mouse genes in the Mouse Genome Informatics (MGI) database. VLAD is available as a web-based application from the MGI web site (http://proto.informatics.jax.org/prototypes/vlad/).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.