Microarray based identification of miR-143 targets. A, The percentages of genes in the up, down and no-change sets with seeds sites in their 3′UTRs. Seed sites were mutually exclusive. Mean log fold-changes were 0.193, −0.004 and −0.249 for the up, down and no-change sets, respectively. The p-values are calculated testing the null hypothesis that the percentages of genes with seed sites are the same for the down-regulated and the up-regulated genes (down vs. up) or the down-regulated genes compared to the no-change genes (down vs. no-change). P-values for 7mer seed site enrichment were 1.2·10 −4 (down vs. up) and 3.5·10 −6 (down vs. no-change). P-values for 7mer-1A seed site enrichment were 1.4·10 −3 (down vs. up) and 1.8·10 −4 (down vs. no-change). P-values for 8mer seed site enrichment were 2.7·10 −11 (down vs. up) and 2.2·10 −16 (down vs. no-change). B, Enriched 7mer words in the 3′UTRs of down-regulated transcripts. Z-scores were calculated as previously described . C, An example of the unbiased word analysis (based on the 1241 genes left after non-specific filtering) showing the running sum of the overrepresentation score for the miR-143 7mer seed site TCATCTC in the list of 3′UTR sequences ranked according to their fold-change (black line) compared to permutations of the ranked gene list (grey lines). D, Quantitative RT-PCR validation of the microarray data. DLD-1 cells were transfected with miR-143 duplex or mock transfected and total RNA harvested 24 h post-transfection. The 3′UTRs of ABHD5 and TAF10 do not contain any miR-143 seed matches, but both genes contain a 8mer seed match in their coding region. All other miR-143 responsive genes contain at least one 7mer seed site in their 3′UTR. The expression level of each transcript data was normalized to HPRT and is shown relative to the level in mock transfected cells. Data are shown as the mean ± S.D. of three replicates.