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. 2006 May 2;4(5):e143. doi: 10.1371/journal.pbio.0040143

Figure 3. Meta-Analysis Identifies Putative Direct Targets of SHR and Their Promoters Are Bound In Vivo by SHR.

Figure 3

(A) Identification of SHR direct targets using meta-analysis. The putative direct targets of SHR were identified by combining the results from three independent experiments: the “direct induction,” “ectopic expression,” and “loss-of-function” (LOF) experiments. The fold change (FC) and p-values for the direct targets in each experiment are shown. Using a meta-analysis approach, the p-values from the three independent approaches were combined, a single meta-analysis p-value was calculated for each gene, and the false discovery rate was then estimated by calculating q-values (meta-analysis q-value). The FC and p-value obtained in the “induction experiment” (Ind) are also indicated.

(B) Demonstration of SHR binding to the promoter regions of the candidate direct targets using ChIP-QRT-PCR (see Materials and Methods).

(C) Tiling of the SCR promoter using ChIP-QRT-PCR. Overlapping primers specific to 200- to 350-bp regions along 1.8 kb of the SCR promoter were used to identify the regions bound by SHR (see Materials and Methods).