Arena3Dweb: interactive 3D visualization of multilayered networks

Karatzas, Evangelos; Baltoumas, Fotis A.; Panayiotou, Nikolaos A.; Schneider, Reinhard; Pavlopoulos, Georgios A.

doi:10.1093/nar/gkab278

Cited by 27 publications

(23 citation statements)

References 55 publications

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“…Table 1 compares OmicsNet 2.0 with several bioinformatics tools including PaintOmics ( 9 ), MergeOmics ( 10 ), OmicsAnalyst ( 8 ), Arena3Dweb ( 11 ), NeDRex ( 16 ) and MetScape ( 17 ). PaintOmics focuses on visual exploration of multi-omics datasets including transcriptomics, metabolomics, region-based data from epigenomics, miRNA and transcription factor, by mapping them to KEGG pathways.…”

Section: Program Description and Methodsmentioning

confidence: 99%

OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics

Zhou

Pang

Lü

et al. 2022

Nucleic Acids Research

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Researchers are increasingly seeking to interpret molecular data within a multi-omics context to gain a more comprehensive picture of their study system. OmicsNet (www.omicsnet.ca) is a web-based tool developed to allow users to easily build, visualize, and analyze multi-omics networks to study rich relationships among lists of ‘omics features of interest. Three major improvements have been introduced in OmicsNet 2.0, which include: (i) enhanced network visual analytics with eleven 2D graph layout options and a novel 3D module layout; (ii) support for three new ‘omics types: single nucleotide polymorphism (SNP) list from genetic variation studies; taxon list from microbiome profiling studies, as well as liquid chromatography–mass spectrometry (LC–MS) peaks from untargeted metabolomics; and (iii) measures to improve research reproducibility by coupling R command history with the release of the companion OmicsNetR package, and generation of persistent links to share interactive network views. We performed a case study using the multi-omics data obtained from a recent large-scale investigation on inflammatory bowel disease (IBD) and demonstrated that OmicsNet was able to quickly create meaningful multi-omics context to facilitate hypothesis generation and mechanistic insights.

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Section: Program Description and Methodsmentioning

confidence: 99%

OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics

Zhou

Pang

Lü

et al. 2022

Nucleic Acids Research

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“…Sequences can be processed by taxonomy assignment pipelines (e.g., PEMA [62]) and be converted into searching PREGO for associations. In addition, network visualization tools, like Arena3D web [63], could allow interactive browsing of associations through multi-layered graphs. Enrichment analyses, like those performed by OnTheFly 2.0 [64] or Flame [65], can be incorporated.…”

Section: Prego Next Stepsmentioning

confidence: 99%

PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

et al. 2022

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To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO’s capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes.

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“…For this purpose, several interactive applications have been implemented and a plethora of review papers have been written [269][270][271][272][273]. Briefly, Cytoscape [39,40], Cytoscape.js [157], Gephi [274], Pajek [275], Ondex [276], Proviz [277], VisANT [278], Osprey [279], Arena3D [280,281], Arena3D web [282], Graphia (Kajeka) [283], NORMA [284], and BioLayout Express 3D [285] are state-of-the-art tools worth mentioning. Similarly, pathway-specific applications include the Pathview [286], BioTapestry [287], PathVisio [214], Interactive Pathways Explorer (iPath) [288], MapMan [289], KEGG [162], Reactome [163], WikiPathways [212] and Pathway Commons [290].…”

Section: Data Visualizationmentioning

confidence: 99%

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

et al. 2021

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Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology.

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Arena3Dweb: interactive 3D visualization of multilayered networks

Cited by 27 publications

References 55 publications

OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics

OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics

PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

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