Genome-Wide Profiling and Analysis of Arabidopsis siRNAs
Figure 8
Analysis of the Affect of rdr2 and dcl3 on the Expression of Cluster-Proximal Genes
(A and B) Fold-change in rdr2 (upper) and dcl3 (lower) versus Col-0 inflorescence plotted the same way as in Figure 6A for cluster-proximal genes (A) and the random gene set (B). Red lines in (A and B) represent mean expression of 1,000 random sets.
(C and D) Natural log (ln) of fold-change in dcl3 plotted versus ln of fold-change in rdr2 for all genes on the ATH1 array (C) or cluster-proximal genes (D). R2 is the square of the Pearson correlation and is the percent variation in rdr2 that is explained by variation in dcl3. Red lines are the best-fit lines.
(E–J) Venn diagram analysis of genes significantly upregulated at least 1.5-fold (SAM false discovery rate = 0.01) in rdr2 or dcl3 and the cluster-proximal gene set (E), dcl1-7 (F), rdr6–15 (G), or all genes with a 24-nt small RNA within 200 nt of the 5′ end (H), within the gene (I), or within 200 nt of the 3′ end (J).