Abstract
BackgroundThe genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However, these databases do not typically include visualization tools and establishing one is not trivial for users who are not computational experts. This, as well as the various formats in which data is commonly deposited, makes the processes of data access, sharing and utility more difficult. Our goal was to provide a simple and user-friendly repository that meets these needs for data-sets from major agricultural crops.DescriptionAgriSeqDB (https://expression.latrobe.edu.au/agriseqdb) is a database for viewing, analysing and interpreting developmental and tissue/cell-specific transcriptome data from several species, including major agricultural crops such as wheat, rice, maize, barley and tomato. The disparate manner in which public transcriptome data is often warehoused and the challenge of visualizing raw data are both major hurdles to data reuse. The popular eFP browser does an excellent job of presenting transcriptome data in an easily interpretable view, but previous implementation has been mostly on a case-by-case basis. Here we present an integrated visualisation database of transcriptome data-sets from six species that did not previously have public-facing visualisations. We combine the eFP browser, for gene-by-gene investigation, with the Degust browser, which enables visualisation of all transcripts across multiple samples. The two visualisation interfaces launch from the same point, enabling users to easily switch between analysis modes. The tools allow users, even those without bioinformatics expertise, to mine into data-sets and understand the behaviour of transcripts of interest across samples and time. We have also incorporated an additional graphic download option to simplify incorporation into presentations or publications.ConclusionPowered by eFP and Degust browsers, AgriSeqDB is a quick and easy-to-use platform for data analysis and visualization in five crops and Arabidopsis. Furthermore, it provides a tool that makes it easy for researchers to share their data-sets, promoting research collaborations and data-set reuse.
Highlights
The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies
Recent advances in generation sequencing (NGS) technologies coupled with decreases in the cost of sequencing have resulted in collection of large volumes of RNA-Seq data from many species [3, 4]
When users are viewing a gene that interests them within GeneView, they can click on a button that directly returns a search from the Gramene database
Summary
The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Recent advances in generation sequencing (NGS) technologies coupled with decreases in the cost of sequencing have resulted in collection of large volumes of RNA-Seq data from many species [3, 4] These data are typically deposited in online repositories in formats that are text and/or table-based. It enables users to view all transcripts from all samples in an experiment, examine trends between samples, to visualize quality-control metrics and to drill down into subsets of transcripts with expression patterns of interest These two data browsers could be integrated to provide users with an easy to use tool for accessing and analysing multiple data-sets and, by developing some enhanced functionality, they could be used for data download and to generating quality images for presentations or publications
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