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psichomics: graphical application for alternative splicing quantification and analysis.

Nuno Saraiva-Agostinho1, Nuno L Barbosa-Morais1

  • 1Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal.

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Summary
This summary is machine-generated.

Psichomics, a new R package, simplifies alternative splicing analysis from RNA-seq data. It aids in identifying splicing signatures and prognostic factors, such as those found in early-stage breast cancer.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Alternative pre-mRNA splicing regulates gene function and cellular processes.
  • Dysregulation of splicing is linked to various diseases.
  • Existing bioinformatics tools for RNA-seq splicing analysis lack user-friendliness and comprehensive features.

Purpose of the Study:

  • To develop an intuitive R package for alternative splicing quantification and downstream analysis.
  • To integrate diverse datasets including TCGA, GTEx, SRA, and user-provided data.
  • To enable comprehensive analysis of splicing, gene expression, and survival.

Main Methods:

  • Development of 'psichomics', an R package with a graphical interface.
  • Utilizing RNA-sequencing (RNA-seq) data for alternative splicing analysis.
  • Incorporating The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Sequence Read Archive (SRA) projects.

Main Results:

  • Psichomics provides user-friendly alternative splicing quantification.
  • The package facilitates dimensionality reduction, differential splicing, gene expression, and survival analyses.
  • Alternative splicing signatures specific to stage I breast cancer were identified.

Conclusions:

  • Psichomics offers an integrated platform for advanced alternative splicing analysis.
  • The tool can uncover novel prognostic factors in diseases like breast cancer.
  • This package enhances the utility of RNA-seq data for clinical and molecular research.