747 / 2019-05-15 12:33:37

Arabidopsis Interactions Viewer 2.0: A multifaceted-integrative client-side web based application for visualizing PSICQUIC protein-protein and protein-DNA interactions

protein-protein interactions,bioinformatics,network biology,data viz,BAR

全体主题 > Systems Biology

The Arabidopsis Interactions Viewer 2.0 (AIV 2.0) is a vast improvement of a former web application (AIV 1.0) which allows a network visualization of 3 million experimentally-validated and 70,000 predicted Arabidopsis protein-protein and protein-DNA interactions curated by the Bio-Analytic Resource (BAR) for Plant Biology. Additional interaction data can also be loaded from other Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) servers such as BioGrid or IntAct. Major technical improvements include using newer, faster technology such as cytoscape.js, allowing a much larger network to be loaded. Moreover, AIV 2.0 integrates multiple facets of biology such as subcellular localization pie-chart overlays, plant gene function terms (MapMan), group-by-localization layouts, DNA Affinity Purification (DAP)-Seq peak link-outs for protein-DNA interactions and filtering by co-expression scores. Multiple export options are available such as exporting to a Cytoscape-tailored JSON and tabular format (CSV) which allows user-defined scripting. To our knowledge, this is the only interactions visualization tool for plant biologists to feature the above facets of biological knowledge. Our goal is therefore to allow researchers use this tool’s multiple data layers to generate new hypotheses relevant to plant biology.