“…METHODS: To overcome the limitations of current methods of analyzing SNP data, the authors used three bipartite analytical representations (bipartite network, heat map with dendrograms, and Circos ideogram) that enable the simultaneous visualization and analysis of subjects, SNPs, and subject attributes. …”
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“…The Ф24(B) genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system. …”
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“…RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. …”
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“…Furthermore, shell OMP separated on 1DE gels were processed using Triple TOF5600 mass spectrometry and 42 proteins of C. hongkongensis and 37 of C. angulata identified. A Circos based comparative analysis of the shell proteins of both oyster species were prepared against the shell proteome of other shell forming gastropods and molluscs to study the evolutionary conservation of OMP and their function. …”
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“…Finally, RISE provides a Circos plot and several table views for integrative visualization, with extensive molecular and functional annotations to facilitate exploration of biological functions for any RRI of interest.…”
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“…It was associated with the stromal and immune populations, especially the monocytic lineage, fibroblasts, and T cells. Circos plots revealed that CD204 was closely associated with many immune checkpoint regulators, especially TIM‐3. …”
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“…Information on gene function and classification was obtained by functional annotation, and circular graph of strain SCCF01 genome, which was created by Circos v0.64. Information on virulence genes (adhesion, flagellum system, exotoxin, and secretory system, etc.) was obtained by virulence genes annotation. …”
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“…MATERIAL/METHODS: Somatic mutation screening was performed using the whole-exome sequencing of osteosarcoma samples, and the distribution of mutations was demonstrated by Circos diagrams. Metascape was used to analyze the GO and KEGG signal pathway enrichment of the genes harboring protein coding alterations, and GeneMANIA was used to analyze the interaction of mutated genes. …”
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“…Additionally, CellCall offers a rich suite of visualization options (Circos plot, Sankey plot, bubble plot, ridge plot, etc.) to present the analysis results. …”
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“…The collected data require analysis (i.e., mining, neural networks, Bayesian networks, and other ML algorithms) before data visualization using Python, R, Circos, Gephi, Tableau, or Cytoscape. Approximately 122 models, all of which were used in FS studies worldwide, were selected from 130 articles. …”
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“…This gene signature could distinguish subpopulations among human SCLC tumors, suggesting its potential clinical utility. Finally, circos plots were constructed to yield a comprehensive view of how transcriptional, copy number and mutational elements affect PLK sensitivity in SCLC cell lines. …”
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“…Furthermore, the prognostic capability of the seven-miRNA signature was demonstrated by receiver operator characteristic curve analysis. A Circos plot was generated to examine the network of genes and pathways predicted to be targeted by the seven-miRNA signature. …”
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“…Genomic alterations in cancer, including CNV and mutations, were represented in Circos. RESULTS: The significantly aberrant CNV segments were found, and the genes involved were associated with the immune system. …”
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“…In addition to human-readable output files, KASPspoon creates Circos configurations that illustrate different in silico and in vitro results. …”
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“…Global methylation status was analyzed and visualized in circular plot by CIRCOS. RNA-and methylation data were correlatively analyzed, and 24 unique genes were identified, for further investigation of regional CpG sites’ interactive patterns by bioconductor package coMET. …”
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“…The hsa_circRNA6448-14-miRNA-mRNA network was drawn using Circos. hsa_circRNA6448-14 was significantly upregulated in ESCC tissues and cell lines. …”
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“…Diversity (alpha and beta diversity) and richness analyses, Circos plots, and principal component analysis (PCA) were also performed. …”
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“…Moreover, four flexible online tools including Genome Browser, Variant Mapper, Circos Plotter and Functional Annotation have been developed to retrieve, visualize and analyze the data. …”
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“…Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. …”
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“…The data were summarized and discussed using Circos plots. RESULTS: Altogether, 42.5% of the reviewed articles were found to be potentially reproducible. …”
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