MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. Export

@article{citeulike:3032984, abstract = {We describe a method, microarray analysis of differential splicing (MADS), for discovery of differential alternative splicing from exon-tiling microarray data. MADS incorporates a series of low-level analysis algorithms motivated by the "probe-rich" design of exon arrays, including background correction, iterative probe selection, and removal of sequence-specific cross-hybridization to off-target transcripts. We used MADS to analyze Affymetrix Exon 1.0 array data on a mouse neuroblastoma cell line after shRNA-mediated knockdown of the splicing factor polypyrimidine tract binding protein (PTB). From a list of exons with predetermined inclusion/exclusion profiles in response to PTB depletion, MADS recognized all exons known to have large changes in transcript inclusion levels and offered improvement over Affymetrix's analysis procedure. We also identified numerous novel PTB-dependent splicing events. Thirty novel events were tested by RT-PCR and 27 were confirmed. This work demonstrates that the exon-tiling microarray design is an efficient and powerful approach for global, unbiased analysis of pre-mRNA splicing.}, author = {Xing, Yi and Stoilov, Peter and Kapur, Karen and Han, Areum and Jiang, Hui and Shen, Shihao and Black, Douglas L. and Wong, Wing Hung H.}, citeulike-article-id = {3032984}, citeulike-linkout-0 = {http://dx.doi.org/10.1261/rna.1070208}, citeulike-linkout-1 = {http://www.rnajournal.org/cgi/content/abstract/14/8/1470}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18566192}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18566192}, day = {1}, doi = {10.1261/rna.1070208}, issn = {1469-9001}, journal = {RNA (New York, N.Y.)}, keywords = {alternative\_splicing, exon\_arrays}, month = {August}, number = {8}, pages = {1470--1479}, posted-at = {2009-11-02 15:15:36}, priority = {2}, title = {MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays.}, url = {http://dx.doi.org/10.1261/rna.1070208}, volume = {14}, year = {2008} }

TY - JOUR ID - citeulike:3032984 L3 - citeulike-article-id:3032984 N2 - We describe a method, microarray analysis of differential splicing (MADS), for discovery of differential alternative splicing from exon-tiling microarray data. MADS incorporates a series of low-level analysis algorithms motivated by the "probe-rich" design of exon arrays, including background correction, iterative probe selection, and removal of sequence-specific cross-hybridization to off-target transcripts. We used MADS to analyze Affymetrix Exon 1.0 array data on a mouse neuroblastoma cell line after shRNA-mediated knockdown of the splicing factor polypyrimidine tract binding protein (PTB). From a list of exons with predetermined inclusion/exclusion profiles in response to PTB depletion, MADS recognized all exons known to have large changes in transcript inclusion levels and offered improvement over Affymetrix's analysis procedure. We also identified numerous novel PTB-dependent splicing events. Thirty novel events were tested by RT-PCR and 27 were confirmed. This work demonstrates that the exon-tiling microarray design is an efficient and powerful approach for global, unbiased analysis of pre-mRNA splicing. IS - 8 JF - RNA (New York, N.Y.) SN - 1469-9001 EP - 1479 TI - MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. VL - 14 SP - 1470 KW - alternative_splicing KW - exon_arrays AU - Xing, Yi AU - Stoilov, Peter AU - Kapur, Karen AU - Han, Areum AU - Jiang, Hui AU - Shen, Shihao AU - Black, Douglas AU - Wong, Wing Hung PY - 2008/08/01/ UR - http://dx.doi.org/10.1261/rna.1070208 ER -