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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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RADPRE: a computational program for identification of differential mRNA processing including alternative

Denghui Xing1, Qingshun Quinn Li

  • 1Department of Biology, Miami University, Oxford, OH, 45056, USA, Denghui.xing@colostate.edu.

Methods in Molecular Biology (Clifton, N.J.)
|December 10, 2014
PubMed
Summary

Alternative polyadenylation (APA) generates multiple transcripts from single genes. RADPRE is an R program that analyzes whole-genome tiling array data to identify differentially processed genes (DPGs) and their false discovery rates (FDRs).

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Alternative polyadenylation (APA) is prevalent in higher eukaryotes, producing multiple transcripts from a single gene.
  • Understanding APA regulation and biological consequences is crucial for deciphering gene expression complexity.

Purpose of the Study:

  • To introduce RADPRE, an R program designed for analyzing whole-genome tiling array data.
  • To identify specific alternative polyadenylation events and differentially processed genes (DPGs) under various conditions.

Main Methods:

  • RADPRE processes whole-genome tiling array data.
  • It includes probe affinity variation correction and a hierarchy of statistical tests.
  • False discovery rate (FDR) estimation for DPGs is performed.

Main Results:

  • The program outputs tabular files detailing DPGs and their associated FDRs.
  • It facilitates the identification of genes with significant APA events.

Conclusions:

  • RADPRE provides a robust method for analyzing APA events using tiling array data.
  • The tool is accessible to scientists with limited programming experience, aiding in the study of gene regulation.