Chromosome View in the Partek Genomics Suite software enables visualization of differential expression and alternative splicing results in RNA-Seq data.
- Select New Track
- Select Add a track from spreadsheet and select 1/transcripts (RNA-Seq_results.transcripts) from the drop-down menu
- Select Next > (Figure 1)
The new track will be added to Chromosome View (Figure 2).
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 - 2017-05-02 (hg19) (-), Legend: Base Colors, and Genome Sequence
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
To further improve our visualization of SLC25A3 isoforms, we can 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
- Move the Isoform proportion track to below the RefSeq Transcripts track by selecting and dragging it up the list (Figure 3)
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 Chromosome View, refer to Visualizing mapped reads with Chromosome View.
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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