Additional data file 10.

Figure S1: comparison between P-value threshold (P < 0.05), q-value threshold (q-value < 0.05) and 2-SD threshold (a signal average < 2 × SD). Figure S2: comparison between 2-SD/P-value threshold and 2-SD/P-value threshold and ChIP/qPCR confirmation. Figure S3: comparison between 2-SD/P-value/q-value threshold and 2-SD/P-value/q-value threshold and ChIP/qPCR confirmation. FDR (q-value) was calculated by using the QVALUE program and R software as described in Materials and methods. The number in parentheses indicates the number of edges excluding auto-perturbation edges. Figure S4: accumulative number of TF-binding positive and negative edges with q-value. Regulatory edges tested for TF-binding were separated into two groups for significance in ChIP assay (ChIP-negative and -positive) and the numbers determined together with the q-values for their perturbations.

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Tomaru et al. Genome Biology 2009 10:R121   doi:10.1186/gb-2009-10-11-r121