Model-based analysis of two-color arrays (MA2C)

Table 2 Numbers and annotation of SDC-3 binding sites detected by different methods

Algorithm	Sample	No. of peaks	In promoter
ChIPOTle	Combined triplicate	1,219	33.63%
MPeak	Replicate 1	1,819	30.35%
	Replicate 2	921	29.32%
	Replicate 3	557	34.11%
MA2C	Combined triplicate (p = 10^-5)	1,181	38.5%
MA2C	Combined triplicate (p = 10^-4)	1,588	35.1%

For annotation, promoter regions 1 kb upstream from translation start sites of genes were used, because the annotation of transcription start sites in C. elegans has not yet been well established.

ISSN: 1474-760X