Motivation: 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 4 probes per exon and no probes for exon-exon junctions, this new junction array averages 8 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 a 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 exons validated out of 173 tested).

Update 140110: The Affymetrix Mouse Exon Junction Array (MJAY) annotation files are available here. Please also replace hjay_reformat.py by mjay_reformat.py.

Author

MADS+ is maintained by the Xing Lab. It is written by Yi Xing and Shihao Shen.

Feedback

Correspondences regarding the MADS+ algorithm should be directed to Prof. Yi Xing (yi-xing at uiowa.edu). Technical questions of running the MADS+ source code should be directed to Prof. Yi Xing (yi-xing at uiowa.edu) and Shihao Shen (shihao-shen at uiowa.edu).

Sample output of MADS+: SLK cassette exon. The red lines indicate the average gene expression levels of SLK in 4 replicate samples transduced with empty vector (EV) or ESRP1. The individual blue lines indicate the average background-corrected intensities of individual probes in a probeset. All the MADS+ p values (+1.24e-8, +1.13e-26, +2.43e-23, -5.41e-9) are shown below the names of the probesets. The p value of 'skip' probeset is at the opposite direction of the p values of 'include' probesets (upstream=upstream 'include' exon-exon junction probeset, downstream=downstream 'include' exon-exon junction probeset, exon=exon probeset). The HJAY array data indicate significantly elevated exon inclusion of SLK exon 13 in response to ESRP1 overexpression.