The Genome Viewer in the Partek Genomics Suite software enables visualization of differential expression and alternative splicing results in RNA-Seq data. 

• With the transcripts spreadsheet selected, select Plot Chromosome View under the Visualization section of the RNA-Seq workflow to launch the Genome Viewer tab with the analyzed results (Figure 1)
  
  

Figure 1. Viewing isoform proportion track in Genome Viewer

The viewer is almost identical to that seen after importing the aligned reads; the difference is the inclusion of the Isoform Proportions track (highlighted in the Tracks list in Figure 1). Next, we are going to view a single gene, SLC25A3, with differentially expressed isoforms. 

• Type SLC25A3 in the Plot Position bar at the top of the window and hit Enter. The browser will browse to the gene (Figure 2)
  
  

Figure 2. Browsing to SLC25A3 in Genome Viewer

At this point, you may find it useful to alter track properties. Each track can be individually configured. For example, isoform information will be easier to visualize if we remove a few tracks. 

• Select Cytoband (hg19) in the Tracks panel 
• Select Remove Track to remove it form the viewer
• Repeat for Genomic Label, RefSeq Transcripts - 2014-01-03 (ht19) (-), and Legend: Base Colors

To further improve our visualization of SLC25A3 isoforms, we can also modify the remaining tracks.

• Select RefSeq Transcripts - 2014-01-03 (hg19) (+) from the Tracks panel
• Change Track height to 60 using the slider
• Select Apply to change track height
• Repeat steps to set each Bam Profile track to a height of 40 to complete our changes (Figure 3)
  
  

Figure 3. Changing tracks in Genome Viewer to facilitate visual analysis of isoform porportions

The Muscle, Brain, Heart, Liver, and genomic label tracks were described in a previous section. Here, the focus is on the Isoform proportion track, which visualizes differential expression and alternative splicing. The reads that are mapped to a certain sample and the proportion of the transcript expressed in that sample are colored to match the Bam Profile track of that sample. In this screenshot, Brain is yellow, Heart is green, Liver is red, and Muscle is orange

SLC25A3 was reported by Wang, et al., (Nature, 2008) to have “mutually exclusive exons (MXEs)”. The reads mapped to the 3 transcripts of this gene in each of the tissue samples are shown in the Genome Viewer in the isoform proportion track. The relative abundances of the individual transcripts of this gene are shown by the height of the color coded bars on each transcript in the isoform proportion track. Note transcript NM_213611 has low expression while transcripts NM_005888 and NM_002635 have higher expression. Also note that NM_005888 is expressed primarily in the heart and muscle, indicated by the primarily green and orange bars, while NM_002635 is expressed primarily in the brain and liver, indicated by the primarily yellow and red bars.  

For additional tips on using the Genome Viewer, refer to Visualizing mapped reads with Genome Viewer.  

References

Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P., & Burge, C.B. Alternative isoform regulation in human tissue transcriptomes. Nature, 2008; 456: 470-6.

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