Visualization & Analyses of the Genomic Data on Gramene’s Ensembl Genome Browsers

Submitted by admin on Wed, 11/28/2012 - 11:21

Figure 1: Gramene homepage

I.   Introduction to Gramene’s Ensembl Genome Browsers

Gramene contains genome browsers for 16 species of flowering plants: Arabidopsis lyrata, Arabidopsis thaliana, Brachypodium distachyon, Brassica rapa, Glycine max, Oryza brachyantha, Oryza glaberrima, Oryza rufipogon, Oryza sativa indica and japonica, Populus trichocarpa, Sorghum bicolor, Setaria italica, Solanum lycopersicum, Vitis vinifera, and Zea mays.

On the Gramene homepage (see Figure 1), users can click on “Genomes” to access the genome browser of their favorite plant species.

The Genome Browser can generate “Karyotype” (chromosome level) views showing distribution of the genes on the chromosomes. Users can quickly identify gene-rich regions within the genome, get an overview of any chromosome, and jump to a (selected) location, which will open a Genome Browser window (see Figure 2) consisting of two panels:

i) The upper panel shows the distribution of genes according to their position on the selected chromosome and their gene IDs.  This panel facilitates scrolling over the chromosome and zooming in/out of a chromosomal region up to visualize gene or nucleotide level details.  Users can further perform detailed queries on genes or gene products of their interest, pull out homologs of a given gene, and view phylogenetic relationships among homologs or members of a gene family, as well as make comparisons across multiple genomes.

Figure 2: Genome Browser window showing details of a selected chromosomal region.

ii) The lower panel shows a detailed view of individual gene(s), the structure of its transcript(s)/gene models, and mapping of various data tracks (e.g. ESTs of rice, maize and Arabidopsis, preloaded by Gramene).  Users can choose to display desired tracks by clicking on the ‘configure this page’ button.

II.   Upload and display data on the Gramene Genome Browser

The Genome Browser allows users to upload and visualize genomic datasets (i.e. genome-wide SNP associations, QTLs, linkage studies, ESTs, Microarrays, RNA-Seq and proteomics) that can be mapped onto the genome.  Several sets of genome-wide data can be displayed simultaneously; users can define a threshold value for their data, and thus choose to view only regions that cross the threshold.

i).    Supported file formats are: BED / BedGraph / Generic / GFF/GTF / PSL / WIG / BAM/ BigWig / VCF

For more information on type of the supported file formats by genome browser, see http://www.gramene.org/info/website/upload/index.html

Figure 3: uploading data on Genome Browser.

ii).        Steps for uploading User Data on Genome Browser

1.  Go to Gramene.org

2.  Click on the “Genome”

3.  Select your favorite plant species (i.e. Vitis vinifera) --> the grape genome browser page opens.

4.  Click on “Manage your data” (left side panel)

5.  Choose “Upload Data” --> upload a file from either, your local computer or from a server using an URL construct

iii).       Steps for displaying your data on the Genome Browser

Once the data file is uploaded successfully, users can display their data using the following steps:

  1. Click on the “Configure this page” (see left side panel)
  2. Click on “Your data” (see left side panel) -->a popup window opens
  3. Click on a small box next to your data/track name and select wiggle plot--> close this window --> it will automatically your data is loaded on the Genome Browser

iv). Display of Data on Genome Browser

Figure 4: Display of gene expression data on Vitis vinifera Genome Browser. The microarray datasets used here was generated in the laboratory of our collaborator Dr. Laurent Deluc at Oregon State University from grape berries encompassing various stages of fruit development and ripening. RNA-Seq (RPKM) data (Zenoni et. al. (2010): Plant Physiol. 152:1787-1795) obtained from three developmental stages of grape berry was also used for comparison.

To illustrate the utility of the Genome Browser, in this post we have used a publicly available RNA-Seq gene expression data published by Zenoni et al. (2010), and microarray data from our collaborator Dr. Laurent Deluc (Oregon State University) to visualize on the Vitis vinifera Genome Browser (see Figure 4). One can zoom in or out to see the expression profile of the genes within a selected chromosome, view expression values, and obtain the most updated information about a gene.