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RADPRE: A Computational Program for Identification of Differential mRNA Processing Including Alternative Polyadenylation

  • Denghui XingEmail author
  • Qingshun Quinn Li
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1255)

Abstract

Genome-wide studies revealed the prevalence of multiple transcripts resulting from alternative polyadenylation (APA) of a single given gene in higher eukaryotes. Several studies in the past few years attempted to address how those APA events are regulated and what the biological consequences of those regulations are. Common to these efforts is the comparison of unbiased transcriptome data, either derived from whole-genome tiling array or next generation sequencing, to identify the specific APA events in a given condition. RADPRE (Ratio-based Analysis of Differential mRNA Processing and Expression) is an R program, developed to serve such a purpose using data from the whole-genome tilling array. RADPRE took a set of tilling array data as input, performed a series of calculation including a correction of the probe affinity variation, a hierarchy of statistical tests and an estimation of the false discovery rate (FDR) of the differentially processed genes (DPG). The result was an output of a few tabular files including DPG and their corresponding FDR. This chapter is written for scientists with limited programming experiences.

Key words

Alternative polyadenylation, Posttranscriptional processing RADPRE Tiling array 

Notes

Acknowledgement

The authors appreciate the original contributions of Jianti Zheng and Guoli Ji. The project was supported by grants from US National Science Foundation (grant nos. IOS–0817829 and IOS-1353354 to QQL), and from Ohio Plant Biotech Consortium (to QQL and DX).

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of BiologyMiami UniversityOxfordUSA
  2. 2.Department of BiologyColorado State UniversityFort CollinsUSA

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