Zhang, XuByrnes, Jake KGal, Thomas SLi, Wen-HsiungBorevitz, Justin O2015-12-142015-12-141465-6906http://hdl.handle.net/1885/94997Whole genome tiling arrays are a key tool for profiling global genetic and expression variation. In this study we present our methods for detecting transcript level variation, splicing variation and allele specific expression in Arabidopsis thaliana. We also developed a generalized hidden Markov model for profiling transcribed fragment variation de novo. Our study demonstrates that whole genome tiling arrays are a powerful platform for dissecting natural transcriptome variation at multi-dimension and high resolution.We thank Andrew Cal for reading the manuscript. XZ was supported by start-up funds to JOB and a NIH grant (R01GM073822) to JOB. JKB was supported by the Department of Education's Graduate Assistance in Areas of National Needs (P-P200A030043) and NIH grants (GM30998 and GM081724) to W-HL. W-HL was supported by NIH grants (GM30998 and GM081724). JOB was supported by a NIH grant (R01GM073822).17 pages© 2008 Zhang et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.alternative splicingarabidopsisgene expression regulation, plantmarkov chainsgene expression profilinggenome, plantpolymorphism, genetic2008-11-2410.1186/gb-2008-9-11-r1652016-02-24