MADS: a New and Improved Method for Analysis of Differential Alternative Splicing by Exon-tiling Microarrays

ABSTRACT: We describe a method, MADS (Microarray Analysis of Differential Splicing), for discovery of differential alternative splicing from exon tiling microarrays. 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 PTB. From a list of exons with pre-determined 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 proc

ORGANISM(S): Mus musculus

SUBMITTER: Yi Xing 

PROVIDER: E-GEOD-11344 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress