InCHlib – interactive cluster heatmap for web applications

Škuta, Ctibor; Bartůněk, Petr; Svozil, Daniel

doi:10.1186/s13321-014-0044-4

Cited by 51 publications

(34 citation statements)

References 54 publications

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“…In order to enable more detailed BC comparisons, we are introducing the capability to dynamically build BC heatmaps based on Pfam annotations. This is achieved through an implementation of the InCHlib Javascript library (16). Cells in the heatmap represent counts of Pfams (columns) found in selected BCs (rows).…”

Section: New Features and Updatesmentioning

confidence: 99%

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

et al. 2016

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Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.

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Section: New Features and Updatesmentioning

confidence: 99%

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

et al. 2016

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“…The visualisation functionality comes from InChLib 15 . The clustering itself is carried out using the HClust R function on the server side.…”

Section: Resultsmentioning

confidence: 99%

Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates

Nyström-Persson

Natsume-Kitatani

Igarashi

et al. 2017

Sci Rep

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Toxygates was originally released as a user-friendly interface to enhance the accessibility of the large-scale toxicogenomics database, Open TG-GATEs, generated by the Japanese Toxicogenomics Project. Since the original release, significant new functionality has been added to enable users to perform sophisticated computational analysis with only modest bioinformatics skills. The new features include an orthologous mode for data comparison among different species, interactive clustering and heatmap visualisation, enrichment analysis of gene sets, and user data uploading. In a case study, we use these new functions to study the hepatotoxicity of peroxisome proliferator-activated receptor alpha (PPARα) agonist WY-14643. Our findings suggest that WY-14643 caused hypertrophy in the bile duct by intracellular Ca2+ dysregulation, which resulted in the induction of genes in a non-canonical WNT/Ca2+ signalling pathway. With this new release of Toxygates, we provide a suite of tools that allow anyone to carry out in-depth analysis of toxicogenomics in Open TG-GATEs, and of any other dataset that is uploaded.

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“…Venn diagrams are displayed thanks to the Jvenn library (15). Interactive heatmaps are built with the Inchlib JavaScript and python libraries (16). Alignments are displayed with the BioJs MSA viewer library (17).…”

Section: Methodsmentioning

confidence: 99%

Family-Companion: analyse, visualise, browse, query and share your homology clusters

Cottret

Briand

Rancurel

et al. 2018

Preprint

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Identifying homology groups in predicted proteomes from different biological sources allows biologists to address questions as diverse as inferring species-specific proteins or retracing the phylogeny of gene families. Nowadays, command-line software exists to infer homology clusters. However, computing and interpreting homology groups with this software remains challenging for biologists and requires computational skills. We propose Family-Companion, a web server dedicated to the computation, the analysis and the exploration of homology clusters. Family-Companion aims to fill the gap between analytic software and databases presenting orthologous groups based on a set of public data. It offers a user-friendly interface to launch or upload precomputed homology cluster analysis, to explore and share the results with other users. The exploration of the results is highly facilitated by interactive solutions to visualize proteome intersections via Venn diagrams, phylogenetic trees, multiple alignments, and also by querying the results by blast or by keywords. Family-Companion is available at http://family-companion.toulouse.inra.fr with a demo dataset and a set of video tutorials. Source code and installation protocol can be found at https://framagit.org/BBRIC/family-companion/. A container-based package simplifies the installation of the web-suite.

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InCHlib – interactive cluster heatmap for web applications

Cited by 51 publications

References 54 publications

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates

Family-Companion: analyse, visualise, browse, query and share your homology clusters

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