What's New at Araport

Araport (https://www.araport.org) aims to to provide Arabidopsis and plant scientists with a new generation web-based data platform. In Araport, users can easily search, analyze, and download a wide array of data through the core components ThaleMine and JBrowse. Araport has also recently released an extensive annotation update, Araport11, for the Col-0 reference genome.

We will demonstrate the powerful ThaleMine data warehouse for browsing the latest genome annotation, integrated with RNA-seq expression, coexpression, physical and genetic interactions, pathways, seed stocks, publications, and more. ThaleMine also provides a user-friendly interface for running gene list enrichment analysis, building data queries, exporting data tables, and saving/sharing work. Araport11 represents a comprehensive update for both structural and functional assignments of gene models using over 100 public RNA-seq datasets. The update included validating/adding splice isoforms, and genomic features such as novel transcribed regions, non-coding gene classes, upstream open reading frames (uORFs), and pseudogenes.

To further enhance data sharing by community members using Araport, the next phase of our project will include developing simple ways for users to automatically integrate their data sets including metadata with Araport for easy discovery and reuse by other researchers. For example, users would be able to create data tracks in the Araport JBrowse for public sharing (e.g. RNA-seq alignments or expression profiles, community genome annotation, other genomic features), simply by providing the appropriate GFF or BAM file along with its associated metadata.

Araport is supported by the NSF and the BBSRC.