Table 2.
Predicated conserved RNA-binding motifs in selectively methylated genes (SMGs)
| Callus | Leaf | |
|---|---|---|
| Common methylated genes (peaks) | 6,185 (11,927|19,215) | |
| Selective methylated genes (peaks) | 626(1,045) | 5,509 (11,820) |
| Peaks for motif findinga | 1,001 | 1,680 (ratio ≥ 16) |
| De-novo conserved motif predictionb (by MEME) | RAGRAG (E-value: 2.8e-075) (252 sites) | UGUAMM (E-value:8.6e-012) (580 sites) |
| Compared to known RBP motifsc (by TOMTOM) | (RAGRAG) | (UGUAMM) |
| P-value | 7.32e-04 | 3.05e-05 |
| E-value | 0.178 | 7.44e-03 |
| q-value | 0.271 | 0.014 |
Note: aThe m6A modification peaks located in intronic regions are filtered out both in callus and leaf, and we choose top 1,680 peaks in leaf depending on the enrichment values; bThe predicted conserved motifs are showed in IUPAC type; cMotifs in the bottom panel are those we found using MEME, and the top panel (RNCMPT00060 represents PUM; RNCMPT00104 represents RNP4F) are those RBP motifs recorded in cisBP-RNA database (http://cisbp-ran.ccbr.utoronto.ca/).