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dc.contributor.authorGhosh, Srinka
dc.contributor.authorHirsch, Heather A.
dc.contributor.authorSekinger, Edward A.
dc.contributor.authorKapranov, Philipp
dc.contributor.authorStruhl, Kevin
dc.contributor.authorGingeras, Thomas R.
dc.date.accessioned2011-04-18T04:51:30Z
dc.date.issued2007
dc.identifier.citationGhosh, Srinka, Heather A. Hirsch, Edward A. Sekinger, Philipp Kapranov, Kevin Struhl, and Thomas R. Gingeras. 2007. Differential analysis for high density tiling microarray data. BMC Bioinformatics 8: 359.en_US
dc.identifier.issn1471-2105en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:4853428
dc.description.abstractBackground: High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. These arrays are being increasingly used to study the associated processes of transcription, transcription factor binding, chromatin structure and their association. Studies of differential expression and/or regulation provide critical insight into the mechanics of transcription and regulation that occurs during the developmental program of a cell. The time-course experiment, which comprises an in-vivo system and the proposed analyses, is used to determine if annotated and un-annotated portions of genome manifest coordinated differential response to the induced developmental program. Results: We have proposed a novel approach, based on a piece-wise function – to analyze genome-wide differential response. This enables segmentation of the response based on protein-coding and non-coding regions; for genes the methodology also partitions differential response with a 5' versus 3' versus intra-genic bias. Conclusion: The algorithm built upon the framework of Significance Analysis of Microarrays, uses a generalized logic to define regions/patterns of coordinated differential change. By not adhering to the gene-centric paradigm, discordant differential expression patterns between exons and introns have been identified at a FDR of less than 12 percent. A co-localization of differential binding between RNA Polymerase II and tetra-acetylated histone has been quantified at a p-value < 0.003 it is most significant at the 5' end of genes, at a p-value < 10^{-13}. The prototype R code has been made available as supplementary material [see Additional file 1].en_US
dc.language.isoen_USen_US
dc.publisherBioMed Centralen_US
dc.relation.isversionofdoi:10.1186/1471-2105-8-359en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2231405/pdf/en_US
dash.licenseLAA
dc.subjectfalse discovery rateen_US
dc.subjectfactor-binding sitesen_US
dc.subjectgene-expressionen_US
dc.subjectchromatin immunoprecipitationen_US
dc.subjectchip-chipen_US
dc.subjectgenomeen_US
dc.subjectstatisticsen_US
dc.subjectarraysen_US
dc.subjectratesen_US
dc.subjecthuman-chromosome-21en_US
dc.titleDifferential analysis for high density tiling microarray dataen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalBMC Bioinformaticsen_US
dash.depositing.authorStruhl, Kevin
dc.date.available2011-04-18T04:51:30Z
dash.affiliation.otherHMS^Biological Chemistry and Molecular Pharmacologyen_US
dc.identifier.doi10.1186/1471-2105-8-359*
dash.contributor.affiliatedStruhl, Kevin


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