MADS+: discovery of differential splicing events from Affymetrix exon junction array data.
Bioinformatics
; 26(2): 268-9, 2010 Jan 15.
Article
em En
| MEDLINE
| ID: mdl-19933160
ABSTRACT
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 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). AVAILABILITY:
MADS+ scripts, documentations and annotation files are available at http//www.medicine.uiowa.edu/Labs/Xing/MADSplus/.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Software
/
Éxons
/
Processamento Alternativo
/
Análise de Sequência com Séries de Oligonucleotídeos
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Ano de publicação:
2010
Tipo de documento:
Article