mRNA Magic™ Feature Overview
This is a brief overview of a few of the features in mRNA Magic™, Jivan's software tool for analyzing mRNA transcriptome sequencing data.
Complete documentation is available in the Help menu after you launch the application.
Introduction
mRNA Magic™ is a software application built from the ground up specifically to find and quantify changes in mRNA variants from transcriptome sequencing and expression data. Whereas gene expression analysis commonly ignores mRNA variants from splicing by averaging data from all regions of a gene, the goal of mRNA splicing analysis is to distinguish between changes in transcription and splicing regulation. mRNA Magic™ provides the power to explore both levels of biological function.
Complete documentation of mRNA Magic™ features can be found in the Help menu after launching the software.
mRNA Splicing Analysis vs. Gene Expression Analysis
Conceptually, mRNA Magic™ differs from simple gene expression software based on reads per kilo base (rpkb). Jivan's scientists and software engineers built mRNA Magic™ around a fundamental equation:
Signal = Gene Expression + Splicing Regulation
In other words, each read potentially provides information about splicing as well as changes in transcription. A core goal of splicing analysis is to clearly separate the two biological processes. Whereas gene expression analysis focuses only on the first process, splicing analysis focuses on both. Splice sites matter within the context of the gene model.
Advantages over gene expression software:
- More accurate gene expression measurement: mRNA Magic™ considers multiple splice variants of a gene and measures gene expression as the sum of expression levels of all splice variants. Jivan's software design recognizes multiple splice sites per gene.
- Identifies changes in RNA splicing: mRNA Magic™ enables you to search for splice events by type, such as exon skip, alternative first exon, alternative last exon, alternative acceptor or donor splice site, or intron retention.
Figure 2. mRNA Magic™ provides a convenient and flexible
form to search your data by splice event. Shown is a search
for exon skips occurring in the middle of the gene model.
For convenience, mRNA Magic™ can generate a complete report of splicing and gene expression changes with just a few clicks of the mouse.
Sample Comparisons
mRNA Magic™ supports two-sample comparison, two-category comparison, paired sample analysis, and multi-sample profiling.
mRNA Magic™ allows you to find splicing changes that occur in some minimum number of samples, such as 3 out of 20. See Figures 2 and 3, which include a drop-down box labeled "Evidence".