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Identification and visualization of differential isoform expression in RNA-seq time series
María José Nueda1, Jordi Martorell-Marugan2, Cristina Martí2
1Mathematics Department, University of Alicante, Alicante 03690, Spain.
Bioinformatics (Oxford, England)
|October 3, 2017
Summary
This study introduces Iso-maSigPro, a new R package for analyzing transcriptomics time series data. It identifies differential isoform usage across time and offers clustering and visualization tools for expression patterns.
Area of Science:
- Transcriptomics
- Bioinformatics
- Statistical Genetics
Background:
- Advancements in sequencing technologies enable detailed analysis of gene transcripts.
- Complex experimental designs, like longitudinal studies, require sophisticated statistical methods.
- Analyzing isoform expression changes in time series data presents a significant challenge.
Purpose of the Study:
- To develop novel statistical methods for analyzing isoform expression changes in time series transcriptomics data.
- To introduce Iso-maSigPro, an R package extending the maSigPro functionality for time series transcriptomics.
- To provide tools for identifying differential isoform usage and analyzing isoform expression patterns over time.
Main Methods:
- Development of Iso-maSigPro, a new functionality within the R package maSigPro.
- Implementation of statistical methods for identifying differential isoform usage across time points.
- Inclusion of clustering and visualization functions for isoform expression patterns.
Main Results:
- Iso-maSigPro successfully identifies genes with differential isoform usage in time series data.
- The package provides effective clustering of genes with similar isoform expression patterns.
- Visualization tools aid in identifying shifts in major expressed isoforms over time.
Conclusions:
- Iso-maSigPro offers a robust solution for analyzing isoform expression dynamics in time series transcriptomics.
- The package facilitates a deeper understanding of gene regulation and function over time.
- Iso-maSigPro is a valuable tool for researchers studying temporal gene expression changes at the isoform level.
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