MADS+: discovery of differential splicing events from Affymetrix exon junction array data.

Bioinformatics
Shihao ShenYi Xing

Abstract

The Affymetrix Human Exon Junction Array is a newly designed high-density exon-sensitive microarray for global analysis of alternative splicing. Contrary to the Affymetrix exon 1.0 array, which only contains four probes per exon and no probes for exon-exon junctions, this new junction array averages eight probes per probeset targeting all exons and exon-exon junctions observed in the human mRNA/EST transcripts, representing a significant increase in the probe density for alternative splicing events. Here, we present MADS+, a computational pipeline to detect differential splicing events from the Affymetrix exon junction array data. For each alternative splicing event, MADS+ evaluates the signals of probes targeting competing transcript isoforms to identify exons or splice sites with different levels of transcript inclusion between two sample groups. MADS+ is used routinely in our analysis of Affymetrix exon junction arrays and has a high accuracy in detecting differential splicing events. For example, in a study of the novel epithelial-specific splicing regulator ESRP1, MADS+ detects hundreds of exons whose inclusion levels are dependent on ESRP1, with a RT-PCR validation rate of 88.5% (153 validated out of 173 tested). MADS+ sc...Continue Reading

References

Jan 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·C Li, W H Wong
Apr 26, 2007·Genome Biology·Tyson A ClarkJohn E Blume
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Mar 17, 2009·Molecular Cell·Claude C WarzechaRuss P Carstens

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Citations

May 13, 2010·Human Molecular Genetics·Lan LinYi Xing
Feb 23, 2012·Molecular and Cellular Biology·Kimberly A DittmarRussell P Carstens
Mar 14, 2014·Nucleic Acids Research·Paolo ConvertiniStefan Stamm
May 21, 2014·ELife·Magdalena M MaslonJavier F Cáceres
May 15, 2013·Statistics in Biosciences·Wei Sun, Yijuan Hu
Jul 7, 2015·Scientific Reports·Junhee SeokWenzhong Xiao
Aug 17, 2010·The EMBO Journal·Claude C WarzechaRuss P Carstens
Nov 13, 2010·Trends in Cell Biology·Frank Gertler, John Condeelis
Jun 12, 2018·Molecular Neuropsychiatry·Marquis Philip VawterTerry W Osborn

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Software Mentioned

HJAY
Ensembl
R
Affymetrix
Linux
Python
MADS
ProbeEffects
Unix
ProbeSelect

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