MOTIVATION: High-density DNA tiling microarrays are a powerful tool for the characterization of complete transcriptomes. The two major analytical challenges are the segmentation of the hybridization signal along genomic coordinates to accurately determine transcript boundaries and the adjustment of the sequence-dependent response of the oligonucleotide probes to achieve quantitative comparability of the signal between different probes. RESULTS: We describe a dynamic programming algorithm for finding a globally optimal fit of a piecewise constant expression profile along genomic coordinates. We developed a probe-specific background correction and scaling method that employs empirical probe response parameters determined from reference hybridizations with no need for paired mismatch probes. This combined analysis approach allows the accurate determination of dynamical changes in transcription architectures from hybridization data and will help to study the biological significance of complex transcriptional phenomena in eukaryotic genomes. AVAILABILITY: R package tilingArray at http://www.bioconductor.org.
MOTIVATION: High-density DNA tiling microarrays are a powerful tool for the characterization of complete transcriptomes. The two major analytical challenges are the segmentation of the hybridization signal along genomic coordinates to accurately determine transcript boundaries and the adjustment of the sequence-dependent response of the oligonucleotide probes to achieve quantitative comparability of the signal between different probes. RESULTS: We describe a dynamic programming algorithm for finding a globally optimal fit of a piecewise constant expression profile along genomic coordinates. We developed a probe-specific background correction and scaling method that employs empirical probe response parameters determined from reference hybridizations with no need for paired mismatch probes. This combined analysis approach allows the accurate determination of dynamical changes in transcription architectures from hybridization data and will help to study the biological significance of complex transcriptional phenomena in eukaryotic genomes. AVAILABILITY: R package tilingArray at http://www.bioconductor.org.
Authors: Aurélie Lardenois; Yuchen Liu; Thomas Walther; Frédéric Chalmel; Bertrand Evrard; Marina Granovskaia; Angela Chu; Ronald W Davis; Lars M Steinmetz; Michael Primig Journal: Proc Natl Acad Sci U S A Date: 2010-12-13 Impact factor: 11.205
Authors: W Clay Spencer; Georg Zeller; Joseph D Watson; Stefan R Henz; Kathie L Watkins; Rebecca D McWhirter; Sarah Petersen; Vipin T Sreedharan; Christian Widmer; Jeanyoung Jo; Valerie Reinke; Lisa Petrella; Susan Strome; Stephen E Von Stetina; Menachem Katz; Shai Shaham; Gunnar Rätsch; David M Miller Journal: Genome Res Date: 2010-12-22 Impact factor: 9.043
Authors: Gard O S Thomassen; Alexander D Rowe; Karin Lagesen; Jessica M Lindvall; Torbjørn Rognes Journal: PLoS One Date: 2009-06-17 Impact factor: 3.240