MADS+: discovery of differential splicing events from Affymetrix exon junction array data.
MADS+: discovery of differential splicing events from Affymetrix exon junction array data.
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DOI：
10.1093/bioinformatics/btp643
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发表时间：
2010-01-15
期刊：
影响因子：
--
通讯作者：
Xing Y
中科院分区：
文献类型：
--
作者：
Shen S;Warzecha CC;Carstens RP;Xing Y
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/. Contact: yi-xing@uiowa.edu
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DOI：
10.1073/pnas.011404098
发表时间：
2001-01-02
影响因子：
11.1
作者：
Li, C;Wong, WH
通讯作者：
Wong, WH
影响因子：
12.3
作者：
Laajala E;Aittokallio T;Lahesmaa R;Elo LL
通讯作者：
Elo LL
影响因子：
4.5
作者：
Xing, Yi;Stoilov, Peter;Wong, Wing Hung
通讯作者：
Wong, Wing Hung
影响因子：
3.7
作者：
Xing, Yi;Kapur, Karen;Wong, Wing Hung
通讯作者：
Wong, Wing Hung
影响因子：
12.3
作者：
Clark TA;Schweitzer AC;Chen TX;Staples MK;Lu G;Wang H;Williams A;Blume JE
通讯作者：
Blume JE