Additional file 4.

Table S2 - ChIP-seq reproducibility. To determine the reproducibility of the ChIP-seq data, we used the method of evaluating replicates as described in the ENCODE Standards document [53]. Briefly, the ENCODE consortium rules are as follows: '80% of the top 40% of the targets identified in one replicate should be contained within the list of targets from the other replicate'. This metric was chosen based on experiences of all the ENCODE production groups to allow an achievable threshold of reproducibility while producing high quality target lists. All ChIP-seq data for site-specific factors submitted to the UCSC browser as part of ENCODE have to pass this quality metric and, as can be seen in Table S2, all of the TCF7L2 data in our manuscript have passed. We note that the metric for reproducibility of 'broad peak' histone marks (such as H3K4me1) has not yet been established by ENCODE. Due to difficulties in calling peaks for such histone marks, the overlap is sometimes lower than 80%.

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Frietze et al. Genome Biology 2012 13:R52   doi:10.1186/gb-2012-13-9-r52