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Polyadenylation in Plants

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Cover of 'Polyadenylation in Plants'

Table of Contents

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    Book Overview
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    Chapter 1 Computational Analysis of Plant Polyadenylation Signals
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    Chapter 2 Prediction of Plant mRNA Polyadenylation Sites
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    Chapter 3 Extraction of Poly(A) Sites from Large-Scale RNA-seq Data.
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    Chapter 4 Poly(A)-Tag Deep Sequencing Data Processing to Extract Poly(A) Sites
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    Chapter 5 Analysis of Poly(A) Site Choice Using a Java-Based Clustering Algorithm
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    Chapter 6 RADPRE: A Computational Program for Identification of Differential mRNA Processing Including Alternative Polyadenylation
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    Chapter 7 Characterization of plant polyadenylation complexes by using tandem affinity purification.
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    Chapter 8 In vitro analysis of cleavage and polyadenylation in Arabidopsis.
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    Chapter 9 Production, Purification, and Assay of Recombinant Proteins for In Vitro Biochemical Analyses of the Plant Polyadenylation Complex
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    Chapter 10 Detection of Disulfide Linkage by Chemical Derivatization and Mass Spectrometry
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    Chapter 11 Transient Expression Using Agroinfiltration to Study Polyadenylation in Plants
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    Chapter 12 A 3′ RACE Protocol to Confirm Polyadenylation Sites
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    Chapter 13 Phage Display Library Screening for Identification of Interacting Protein Partners
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    Chapter 14 Genome-Wide Determination of Poly(A) Site Choice in Plants
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    Chapter 15 DNA/RNA Hybrid Primer Mediated Poly(A) Tag Library Construction for Illumina Sequencing
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    Chapter 16 Poly(A) Tag Library Construction from 10 ng Total RNA.
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    Chapter 17 A Rapid, Simple, and Inexpensive Method for the Preparation of Strand-Specific RNA-Seq Libraries
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    Chapter 18 Genome-Wide Analysis of Distribution of RNA Polymerase II Isoforms Using ChIP-Seq.
Attention for Chapter 6: RADPRE: A Computational Program for Identification of Differential mRNA Processing Including Alternative Polyadenylation
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Chapter title
RADPRE: A Computational Program for Identification of Differential mRNA Processing Including Alternative Polyadenylation
Chapter number 6
Book title
Polyadenylation in Plants
Published in
Methods in molecular biology, January 2015
DOI 10.1007/978-1-4939-2175-1_6
Pubmed ID
Book ISBNs
978-1-4939-2174-4, 978-1-4939-2175-1
Authors

Denghui Xing, Qingshun Quinn Li

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.

Mendeley readers

The data shown below were compiled from readership statistics for 4 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 4 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 2 50%
Student > Ph. D. Student 1 25%
Professor 1 25%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 2 50%
Agricultural and Biological Sciences 2 50%