Figure 6
From: An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection
mRNA-seq data analysis points to a restricted set of xisRNA cis-genes as potential silencing targets. (A) Distribution of the log2 transform of the fold change ratio for DE analysis records (expressed gene by treatment comparison combinations) contrasted on whether or not the gene has a cognate xisRNA and this xisRNA is also up-regulated in the same treatment comparison. The horizontal lines reflect the 25%, median and 75% quartiles. (B) log2(FC) of xiRNA versus cognate cis-gene in a relevant treatment comparison. For each treatment comparison, a cis-gene is considered to be ‘Induced’ if it has a log2FC > 0 and a p-value ≤ 0.05, ‘Repressed’ if the log2FC < 0 and the p-value ≤ 0.05 and ‘Not significant’ otherwise. (C) Histogram distributions of the variables computed in 20,000 trials for randomization test. (D) Summary of the rice annotated cis-genes whose expression profile is consistent in at least one comparison with a possible negative regulatory effect of a cognate xisRNA. The ‘DE stats consistent with xisRNA silencing status’ is regarded as “TRUE” if in the corresponding comparison, the xisRNA has been detected as induced and if the gene DE record has log2FC < 0 and a p-value ≤ 0.05, “FALSE” if the xisRNA has been detected as induced but the gene DE record does not pass the log2FC or p-value criteria and “NA” (Not Available; white background) otherwise.
