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Graphical display of genes, RNAs, intron-exon structures, splice junctions, and alternative splicing patterns were implemented in RoBuST using Gene Plot, Splice Signal Plot and AS Plot modules from the EuSplice [ 12] project.
Clicking on the variation reveals a pop-up box showing the ID, the genomic coordinates, and a link to the variation tab shown in figure 7. Genome browsers have gone beyond the simple display of genes and transcripts, moving into the integration of biological data.
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The temporal and spatial display of gene expression might reflect the attainment of specialized functions by OsPPs.
WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks.
The tool ProMeTra supports this process by a combined display of gene expression and metabolome data sets on a chosen metabolic or other pathway of biological relevance.
Using differential display of gene expression by microarray analysis, one set of 101 upregulated RA-related genes and one set of 300 gene transcripts considered to be downregulated in RA were detected and are now available for further research.
The Microarray Expression Viewer is a Java based application, created to provide a visual display of gene expression data for a set of selected genes across a set of selected experimental studies.
Predicted gene models were manually inspected using the Integrative Genomics Viewer (IGV) [ 19] that enabled simultaneous display of gene models predicted by AUGUSTUS, Cufflinks and Broad Institute together with RNA-Seq reads.
Although the idea of web-based database tools is not novel, aGFP database offers a quick and interactive display of gene expression profiles using the virtual plant facility as well as alternate more conventional outputs.
Although not a substitute for data submission to databases of record, Badger is a customizable environment for public and collaborative display of gene-centred genomic information, and will aid in preparation for publication and submission.
MapMan displays of genes that are differentially expressed in mature Ved and PS fruits are shown in Figs. 7, 8 and 9.
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