BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications

Cui, Ya; Chen, Xiaowei; Luo, Huaxia; Fan, Zhen; Luo, Jianjun; He, Shunmin; Yue, Haiyan; Zhang, Peng; Chen, Runsheng

doi:10.1093/bioinformatics/btw041

Cited by 123 publications

(83 citation statements)

References 9 publications

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“…The transcriptIDs can be used to cross-reference with Supplemental Data 2 which is a GFF transcript annotation file that contains exon structure for each TE transcript. All TEs and "ExpressedAndAnnotated" TEs are used in the circular BioCircos plot (Cui et al, 2016) shown in Figure 2B.…”

Section: Updating the Tair10 Te Annotationmentioning

confidence: 99%

Long-read cDNA Sequencing Enables a ‘Gene-Like’ Transcript Annotation of Arabidopsis Transposable Elements

Panda

2020

Preprint

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High-quality transcript-based annotations of genes facilitates both genome-wide analyses and detailed single locus research. In contrast, transposable element (TE) annotations are rudimentary, consisting of only information on location and type of TE.When analyzing TEs, their repetitiveness and limited annotation prevents the ability to distinguish between potentially functional expressed elements and degraded copies. To improve genome-wide TE bioinformatics, we performed long-read Oxford Nanopore sequencing of cDNAs from Arabidopsis lines deficient in multiple layers of TE repression. We used these uniquely-mapping transcripts to identify the set of TEs able to generate mRNAs, and created a new transcript-based annotation of TEs that we have layered upon the existing high-quality community standard TAIR10 annotation.The improved annotation enables us to test specific standing hypotheses in the TE field.We demonstrate that inefficient TE splicing does not trigger small RNA production, and the cell more strongly targets DNA methylation to TEs that have the potential to make mRNAs. This work provides a transcript-based TE annotation for Arabidopsis, and serves as a blueprint to reduce the genomic complexity associated with repetitive TEs in any organism.

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Section: Updating the Tair10 Te Annotationmentioning

confidence: 99%

Long-read cDNA Sequencing Enables a ‘Gene-Like’ Transcript Annotation of Arabidopsis Transposable Elements

Panda

2020

Preprint

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“…A related tool, MultiProtScale (Table 2), computes and displays physicochemical properties of amino acids over sequences and alignments, acting as an interactive extension of Expasy's ProtScale tool. Moving on to genomics, SnipViz [32] and BioCircos.js [33] help visualize and disseminate gene and protein sequences and their annotations, while GenomeD3Plot [34] and pileup.js [35] allow for interactive in-browser visualization of genomic data.…”

Section: Javascript Libraries For Online Interactive Data Displaymentioning

confidence: 99%

“…A related tool, MultiProtScale (Table 2), computes and displays physicochemical properties of amino acids over sequences and alignments, acting as an interactive extension of Expasy's ProtScale tool. Moving on to genomics, SnipViz [32] and BioCircos.js [33] help visualize and disseminate gene and protein The cleaned text is then processed with nlp-compromise to calculate frequencies of words and n-grams (word pairs, triplets, etc. ); (C) Example interactive visualization of an alignment of PFAM seed members for COX2 (PF00116) with JSAV [3], achieved through the demonstration webpage at http://www.bioinf.org.uk/software/jsav/.…”

Section: Javascript Libraries For Online Interactive Data Displaymentioning

confidence: 99%

Web Apps Come of Age for Molecular Sciences

Abriata

2017

Informatics

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Whereas server-side programs are essential to maintain databases and run data analysis pipelines and simulations, client-side web-based computing tools are also important as they allow users to access, visualize and analyze the content delivered to their devices on-the-fly and interactively. This article reviews the best-established tools for in-browser plugin-less programming, including JavaScript as used in HTML5 as well as related web technologies. Through examples based on JavaScript libraries, web applets, and even full web apps, either alone or coupled to each other, the article puts on the spotlight the potential of these technologies for carrying out numerical calculations, text processing and mining, retrieval and analysis of data through queries to online databases and web services, effective visualization of data including 3D visualization and even virtual and augmented reality; all of them in the browser at relatively low programming effort, with applications in cheminformatics, structural biology, biophysics, and genomics, among other molecular sciences.

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“…The server frontend is designed using the Bootstrap css framework. The interactive display of the mutation data relies on BioCircos.js (16) and Cytoscape.js (17) javascript libraries, which were modified to fulfill the visualization needs. D3.js (https://d3js.org/) javascript library is also used to display legend information, and Jsmol (http://www.jmol.org/) to provide interactive visualization of protein 3D structures.…”

Section: Server Informationmentioning

confidence: 99%

A PanorOmic view of personal cancer genomes

Mateo

Guitart-Pla

Pons

et al. 2017

Nucleic Acids Research

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The massive molecular profiling of thousands of cancer patients has led to the identification of many tumor type specific driver genes. However, only a few (or none) of them are present in each individual tumor and, to enable precision oncology, we need to interpret the alterations found in a single patient. Cancer PanorOmics (http://panoromics.irbbarcelona.org) is a web-based resource to contextualize genomic variations detected in a personal cancer genome within the body of clinical and scientific evidence available for 26 tumor types, offering complementary cohort- and patient-centric views. Additionally, it explores the cellular environment of mutations by mapping them on the human interactome and providing quasi-atomic structural details, whenever available. This ‘PanorOmic’ molecular view of individual tumors, together with the appropriate genetic counselling and medical advice, should contribute to the identification of actionable alterations ultimately guiding the clinical decision-making process.

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BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 123 publications

References 9 publications

Long-read cDNA Sequencing Enables a ‘Gene-Like’ Transcript Annotation of Arabidopsis Transposable Elements

Long-read cDNA Sequencing Enables a ‘Gene-Like’ Transcript Annotation of Arabidopsis Transposable Elements

Web Apps Come of Age for Molecular Sciences

A PanorOmic view of personal cancer genomes

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