ArticleNucleic acids research2021
Arena3Dweb: interactive 3D visualization of multilayered networks.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 31 citations in OpenAlex.
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- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Exploring animal behaviour multilayer networks in immersive environments - a conceptual framework.Journal of integrative bioinformatics · 2024Article
- Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks.NPJ systems biology and applications · 2024Article
- iTraNet: a web-based platform for integrated trans-omics network visualization and analysis.Bioinformatics advances · 2024Article
- Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources.Bioinformatics (Oxford, England) · 2023Article
- Arena3DNAR genomics and bioinformatics · 2023Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Drug genetic associations with COVID-19 manifestations: a data mining and network biology approach.The pharmacogenomics journal · 2022Article
- NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization.Genomics, proteomics & bioinformatics · 2022Article
- Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining.Biomolecules · 2022Article
- PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types.Microorganisms · 2022Article
- The network makeup artist (NORMA-2.0): distinguishing annotated groups in a network using innovative layout strategies.Bioinformatics advances · 2022Article
- Article
- Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.Frontiers in molecular biosciences · 2022Review
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- Fibrotic expression profile analysis reveals repurposed drugs with potential anti-fibrotic mode of action.PloS one · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Efficient integration and visualization of heterogeneous biomedical information in a single view is a key challenge. In this study, we present Arena3Dweb, the first, fully interactive and dependency-free, web application which allows the visualization of multilayered graphs in 3D space. With Arena3Dweb, users can integrate multiple networks in a single view along with their intra- and inter-layer connections. For clearer and more informative views, users can choose between a plethora of layout algorithms and apply them on a set of selected layers either individually or in combination. Users can align networks and highlight node topological features, whereas each layer as well as the whole scene can be translated, rotated and scaled in 3D space. User-selected edge colors can be used to highlight important paths, while node positioning, coloring and resizing can be adjusted on-the-fly. In its current version, Arena3Dweb supports weighted and unweighted undirected graphs and is written in R, Shiny and JavaScript. We demonstrate the functionality of Arena3Dweb using two different use-case scenarios; one regarding drug repurposing for SARS-CoV-2 and one related to GPCR signaling pathways implicated in melanoma. Arena3Dweb is available at http://bib.fleming.gr:3838/Arena3D or http://bib.fleming.gr/Arena3D.
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.