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Omicsoft is the leading provider of Next Generation Sequencing, Cancer Genomics, Immunology, and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis.

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[New Feature] Exon Junction Curve in Genome Browser to Show Exon Junction Curves Side by Side with Coverage

Vivian Zhang

Alternative Splicing (AS) is a process that exons or noncoding regions within DNA are differentially skipped or joined, resulting in different protein isoforms. This process allows individual genes to encode different mRNAs that encode proteins with diverse and even opposite functions. Alternative splicing has been shown to play an important role in a number of human diseases, including cancer, cardiovascular and neurodegenerative diseases. In Omicsoft Array Studio and Land, we provide modules and visualization functions that make it easier for users to research splicing. One example is the recent implemented function, Show Exon Junction Curve in Omicsoft Genome Browser.

Previously, in Omicsoft Genome Browser, we provide Exon Junction information in each individual track: 

Lung adenocarcinoma sample RNA-Seq data in Genome Browser. The blue lines below the read signal and the numbers indicate the number of exon junction reads. 

Lung adenocarcinoma sample RNA-Seq data in Genome Browser. The blue lines below the read signal and the numbers indicate the number of exon junction reads. 

The Show Exon Junction function allows user to checkout the number of exon junction reads. To better improve the visualization especially in the case of alternative splicing, we implemented Exon Junction Curve function:

Lung adenocarcinoma sample RNA-Seq data in Genome Browser with Exon Junction Curves. The LUAD track represents all lung adenocarcinoma samples. The Solid Tissue Normal and Primary Tumor tracks represent the normal and tumor sample from lung adenocarcinoma subject respectively. 

Lung adenocarcinoma sample RNA-Seq data in Genome Browser with Exon Junction Curves. The LUAD track represents all lung adenocarcinoma samples. The Solid Tissue Normal and Primary Tumor tracks represent the normal and tumor sample from lung adenocarcinoma subject respectively. 

Exon Junction Curve provides better visualization of exon junction events. In above example, it clearly shows the alternative splicing in lung adenocarcinoma samples (Two curves in LUAD track). The height of the curve represents the number of reads scaled to the total reads within the same track. In contrast,  the Solid Tissue Normal and Primary Tumor tracks only have one exon junction curve for each track, implying that differential splicing of PMP22 occurs in tumor and normal samples.