ZENBU Reports

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Nowadays, scientific publications often times come with dedicated websites that manage and organize the data, showcase the analysis results, and offer tools for additional analysis. Such accompanying websites are important both for consortia projects that produce massive genome-wide data sets, and increasingly also for smaller projects with limited resources. Usually, these websites are custom-created for each publication separately, requiring the services and expertise of a software engineer and increasing the maintenance burden as well as data storage needs.

To address this, we change the paradigm of data presentation and data integration by creating ZENBU-Reports. Incorporating concepts from wiki-pages, google-sheets/docs, R-shiny, and page-layout programs, ZENBU-Reports is a new visualization system that enables users to construct a scientific portal website without requiring any programming skills. The portal website created in ZENBU-Reports consists of Reports pages constructed from interactive elements that can be configured and arranged using a graphical interface. ZENBU-Reports provides the graphical elements commonly used in supplementary websites, including ordered lists, tables, scatter plots, bar graphs, network graphs, genome-wide plots, heatmaps, and data-injection html. The resulting website can be saved to a fixed URL for sharing as a reference in scientific publications.

For convenience and to minimize data storage requirements, ZENBU-Reports is built upon the existing ZENBU genome browser, allowing reuse of the same public and private genome-wide data in both systems. Its secured data management and data sharing system lets users share unpublished data and Report pages with a specific collaboration of colleagues only. Upon publication and release of the data, the portal website built using ZENBU-Reports can be opened to the public by toggling a switch, allowing anybody to access and interact with the created pages and data. ZENBU-Reports thus provides a complete solution for the visualization and dissemination of data and analysis results during the full lifespan of a research project.

Examples

The following three examples demonstrate the concept and power of ZENBU-Reports:

This page shows gene loci of interest listed in a table and visualized in a ZENBU genome browser view, where they are colored based on significance. Selecting a locus in the genome-wide view or a gene in the table updates the location shown in the genome-browser. This video shows how to build such a page from scratch and to save it to a URL for public access: https://fantom.gsc.riken.jp/zenbu/reports/zenbu-reports-demo3.mkv

This page shows a scrolling list with gene targets that were knocked down in a large screening project. Upon clicking on a target, Gene-Set-Enrichment-Analysis results are loaded into the table, and the category-filter and the graph linked to the table automatically update. Visitors can interact with the data by altering the category filters, by searching for genes, or by applying cutoff filters.

This page shows differential expression results from the same screening project. Visitors can select a knockdown target to load the experiment details and differential expression results in a table, in three linked scatter plots, as well as in a network graph showing the location both of the target and of the differentially expressed gene loci. Linked page elements update dynamically upon selecting a gene in the table, a point in a scatter plot, or a line in the network graph.

Published examples

Building pages and Configuring elements

  • setting data sources and sharing data between elements

new Edge file types for graphs and networks

  • event triggers to perform linked loading and user event cascades

Available Element types

  • Table & TreeList (custom ZENBU code)
  • ZENBU Genome Browser (new ZENBU3.0 version)
  • Chart (chart.js and Plotly integration)
  • Circos (partial reimplemented in javascript not using the circos perl library)
  • Cytoscape (cytoscape.js integration)
  • GenomeWide (ZENBU code)
  • Category filter (ZENBU code)
  • Signal Filter (ZENBU code)
  • HTML-Element (ZENBU code)