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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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Keeping you up-to-date with the latest in NGS, Bioinformatics Analysis, and cancer genomics with blogs on Array Suite, OncoLand (TCGA and more), ImmunoLand, and more.

[GENOMIC RESEARCH] Identifying Alternative splicing in ImmunoLand

Vivian Zhang

Alternative splicing is a regulated process during gene expression that can produce variant proteins from a single gene. It plays an important role in cellular functions and is closely related to a variety of diseases (1). At Omicsoft, our Land products (ImmunoLand and OncoLand)  allow users to identify splicing events that are associated with diseases, pathological measures or any clinical information. 

Figure 1. Splicing of Serpinb7 in lesional versus non-lesional samples. Different dominant transcripts express in lesional versus non-lesional samples, suggesting the association between serpinb7 splicing and lesion. 

Figure 1. Splicing of Serpinb7 in lesional versus non-lesional samples. Different dominant transcripts express in lesional versus non-lesional samples, suggesting the association between serpinb7 splicing and lesion. 

Interesting in learning how to identify differential splicing, for instance the splicing event of serpinb7 in lesional and non-lesional psoriasis samples? Land Integration Analysis can help.

First, the user can group the SampleSet for the samples of interest using specific disease status, pathological measures or clinical information. Using our newly released ImmunoLand, the user can set the Grouping into Pathology, and then filter lesional and non-lesional samples for display. By selecting all lesional samples, the user can create Lesional Samples vs Non Lesional SampleSet.

Land Integration Analysis allows the user perform differential analysis on expression, splicing, copy number variation and mutation data using SampleSet. For example, by using lesional and non-lesional sample grouping, the user can perform integration analysis trying to identify the splicing event associated with lesional status:

The analysis result reports statistics of Kruskal-Wallis Test, the smaller the p-value (FDR adjusted) is, the stronger the splicing is associated with lesion. In this case, serpinb7 appears to be the top gene:

 

Next, the user can search serpinb7 in ImmunoLand, and then check out RNA-Seq | Genome Browser view, use Omicsoft's powerful Genome Browser functions to generate Figure 1 and visualize the splicing events. A brief search on PubMed shows other exciting work on serpinb7, suggesting its roles in keratosis and carcinoma.