The electronic version of this article is the complete one and can be
found online at http://genomebiology.com/2005/6/11/R96
Chromatin 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'.
F.D.G. and F.P.R. were supported in part by Funds
for Discovery provided by John Taplin and by an institutional grant from the
HHMI Biomedical Research Support Program for Medical Schools. M.P.,
F.D.G., and K.S. were supported by NIH/NIGMS grants GM30186,
GM53720, and NIH/NHGRI grant HG003147. M.P. was supported by an
EMBO Long Term Fellowship and the 'Ramón y Cajal' program of the Spanish
Ministry of Science.
Peer reviewed