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Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization

AutorGibbons, Francis D.; Proft, Markus ; Struhl, Kevin; Roth, Frederick P.
Fecha de publicación1-nov-2005
EditorBioMed Central
CitaciónGenome Biol. 2005; 6(11): R96
ResumenChromatin immunoprecipitation combined with microarray technology (Chip2) allows genomewide determination of protein-DNA binding sites. The current standard method for analyzing Chip2 data requires additional control experiments that are subject to systematic error. We developed methods to assess significance using variance stabilization, learning error-model parameters without external control experiments. The method was validated experimentally, shows greater sensitivity than the current standard method, and incorporates false-discovery rate analysis. The corresponding software ('Chipper') is freely available. The method described here should help reveal an organism's transcription-regulatory 'wiring diagram'.
DescripciónThe electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/11/R96
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Fichero Descripción Tamaño Formato  
picrender.pdfPrincipal257,64 kBAdobe PDFVista previa
gb-2005-6-11-r96-S1.txtAdditional data File 1. A tab-delimited file containing the results of our analysis for all intergenic regions studied in our experiments357,82 kBTextVisualizar/Abrir
gb-2005-6-11-r96-S2.pdfAdditional data File 2. A detailed description of the comparison between the targets of Sko1 identified by Chipper when applied both to the data presented here and to other Chip2 data, and previously published p values using a single-array error model66,45 kBAdobe PDFVista previa
gb-2005-6-11-r96-S3.pdfAdditional data File 3. A figure illustrating the comparisons made in Additional data file 261,87 kBAdobe PDFVista previa
gb-2005-6-11-r96-S4.pdfAdditional data File 4. A figure illustrating the comparisons made in Additional data file 211,26 kBAdobe PDFVista previa
gb-2005-6-11-r96-S5.pdfAdditional data File 5. A figure comparing the two methods described in Additional data file 2 as applied to results from six additional transcription factors50,41 kBAdobe PDFVista previa
gb-2005-6-11-r96-S6.txtAdditional data File 6. A list of the intergenic regions identified as targets3,05 kBTextVisualizar/Abrir
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