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Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

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digeR: a graphical user interface R package for analyzing 2D-DIGE data.

Yue Fan¹, T Brendan Murphy, R William G Watson

¹UCD School of Medicine and Medical Science, UCD Conway Institute of Biomolecular and Biomolecular Research and UCD School of Mathematical Sciences, University College Dublin, Dublin 4, Dublin, Ireland.

Bioinformatics (Oxford, England)

|August 27, 2009

Summary

This summary is machine-generated.

This study introduces digeR, an R package for analyzing 2D Difference In-Gel Electrophoresis (2D-DIGE) data. It aids in biomarker discovery and visualizes protein post-translational modification changes.

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Area of Science:

Proteomics
Bioinformatics

Background:

2D Difference In-Gel Electrophoresis (2D-DIGE) is a standard proteomics method for biomarker discovery.
High-dimensional 2D-DIGE data analysis necessitates multivariate statistical techniques.
Protein post-translational modification (PTM) data is often neglected in 2D gel analysis.

Purpose of the Study:

To present digeR, a user-friendly R package with a graphical interface for 2D-DIGE data analysis.
To enable visual identification of PTM alterations across different biological states.
To support biomarker discovery using multivariate analysis methods.

Main Methods:

Development of the digeR R package with a graphical user interface.
Application of multivariate analysis techniques for high-dimensional proteomics data.
Visual exploration of protein post-translational modification patterns.

Main Results:

The digeR package facilitates the analysis of 2D-DIGE data.
The tool allows for visual inspection of potential PTM changes between biological conditions.
It supports the identification of potential biomarkers through integrated multivariate analysis.

Conclusions:

digeR provides a valuable tool for researchers analyzing 2D-DIGE data.
The package enhances the capability to discover biomarkers by considering PTMs.
It simplifies complex proteomics data analysis and visualization.