Comparison of motif enrichment in peaks identified by ChIP-chip and Chip-Seq. Chi-square test statistics from 2 × 2 contingency table is shown for all 153 families of vertebrate TF binding motif patterns found in the MatBase library 7.0 database of Genomatix (Genomatix, GmBH, Munich, Germany). Motif scan was performed using MatInspector in Genomatix using the default setting. A. STAT1 ChIP-chip result (on about 10% of the entire genome, the majority of them (88%) on chromosomes 20, 21, 22, X and Y). B. STAT1 ChIP-Seq result (subset of 2,023 peaks out of 24,394 located on Chromsome 20, 21, 22, X and Y). C. Correlation between motif enrichment and rank of significance in peaks indentified from STAT1 ChIP-Seq and ChIP-chip experiments. All peaks were ordered according to their significance and then divided into five segments of equal sizes. Their motif enrichment is measured by Chi-square test statistics in these five segments are shown from left to right.
Qin et al. BMC Bioinformatics 2010 11:369 doi:10.1186/1471-2105-11-369