ArticleBMC bioinformatics2013
RCytoscape: tools for exploratory network analysis.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
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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.
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Who cites it
59 citing papers in PubMed.
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- The RIN4-like/NOI proteins NOI10 and NOI11 modulate the response to biotic stresses mediated by RIN4 in Arabidopsis.Plant cell reports · 2024Article
- Investigating the impact of paternal aging on murine sperm miRNA profiles and their potential link to autism spectrum disorder.Scientific reports · 2023Article
- Transcriptome Dynamics ofInternational journal of molecular sciences · 2023Article
- The Arabidopsis thioredoxin TRXh5regulates the S-nitrosylation pattern of the TIRK receptor being both proteins essential in the modulation of defences to Tetranychus urticae.Redox biology · 2023Article
- Assessing the role of the gut microbiome in methylmercury demethylation and elimination in humans and gnotobiotic mice.Archives of toxicology · 2023Article
- Topsoil and subsoil bacterial community assemblies across different drainage conditions in a mountain environment.Biological research · 2023Article
- Heterologous Expression and Characterization of a Full-length Protozoan Nitroreductase from Leishmania orientalis isolate PCM2.Molecular biotechnology · 2023Article
- Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert.Environmental microbiome · 2023Article
- The influence of tissue pH and RNA integrity number on gene expression of human postmortem brain.Frontiers in psychiatry · 2023Article
- Regulation Networks of Non-Coding RNA-Associated ceRNAs in Cisplatin-Induced Acute Kidney Injury.Cells · 2022Article
- Human Gut Mycobiome and Fungal Community Interaction: The Unknown Musketeer in the Chemotherapy Response Status in Bladder Cancer.European urology open science · 2022Article
- Proteomics analysis identifies PEA-15 as an endosomal phosphoprotein that regulates α5β1 integrin endocytosis.Scientific reports · 2021Article
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- Disentangling transcriptional responses in plant defense against arthropod herbivores.Scientific reports · 2021Article
- Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores.Journal of integrative plant biology · 2021Article
- MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets.Nucleic acids research · 2020Article
- Article
- Comparative transcriptome profiling of the response to Pyrenochaeta lycopersici in resistant tomato cultivar Mogeor and its background genotype-susceptible Moneymaker.Functional & integrative genomics · 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiomolecular pathways and networks are dynamic and complex, and the perturbations to them which cause disease are often multiple, heterogeneous and contingent. Pathway and network visualizations, rendered on a computer or published on paper, however, tend to be static, lacking in detail, and ill-equipped to explore the variety and quantities of data available today, and the complex causes we seek to understand.
resultsRCytoscape integrates R (an open-ended programming environment rich in statistical power and data-handling facilities) and Cytoscape (powerful network visualization and analysis software). RCytoscape extends Cytoscape's functionality beyond what is possible with the Cytoscape graphical user interface. To illustrate the power of RCytoscape, a portion of the Glioblastoma multiforme (GBM) data set from the Cancer Genome Atlas (TCGA) is examined. Network visualization reveals previously unreported patterns in the data suggesting heterogeneous signaling mechanisms active in GBM Proneural tumors, with possible clinical relevance.
conclusionsProgress in bioinformatics and computational biology depends upon exploratory and confirmatory data analysis, upon inference, and upon modeling. These activities will eventually permit the prediction and control of complex biological systems. Network visualizations--molecular maps--created from an open-ended programming environment rich in statistical power and data-handling facilities, such as RCytoscape, will play an essential role in this progression.
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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.