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
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 % |
---|---|---|
Agricultural and Biological Sciences | 2 | 50% |
Computer Science | 1 | 25% |
Biochemistry, Genetics and Molecular Biology | 1 | 25% |