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

Francis D Gibbons1, Markus Proft12, Kevin Struhl1 and Frederick P Roth1*

Author Affiliations

1 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, MA 02115, USA

2 Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain

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Genome Biology 2005, 6:R96  doi:10.1186/gb-2005-6-11-r96

Published: 1 November 2005

Abstract

Chromatin immunoprecipitation combined with microarray technology (Chip2) allows genome-wide 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'.