Table 2 Enrichment of PLACE- and PBM-curated cis-regulatory elements (CRE) of selected k-means assigned clusters containing differentially expressed transcripts comparing skins of small and large berries. The table contains detailed information on the number of promoters with the specified CRE, number of promoters in the genome containing the specified CRE, CRE sequence, false discovery rate (FDR), and the designated CRE name and regulatory description. A full description on the corresponding genes containing the associated CRE is available in Additional file 1: Table S4
Cluster | Matches in sample | Matches in genome | FDR | Motif | Motif name | Regulation |
|---|---|---|---|---|---|---|
1 | 92 | 3331 | 9.67E-06 | ACGTGKC | ACGTABREMOTIFA2OSEM | ABRE |
146 | 6199 | 9.67E-06 | CACGTG | CACGTGMOTIF | bHLH/bZIP | |
98 | 4120 | 0.000552 | AGATATTT | CCA1-1 | MYB-related | |
33 | 1008 | 0.0024 | YACGTGGC | ABREATCONSENSUS | ABRE | |
54 | 2115 | 0.004942 | CACGTGG | IRO2OS | bHLH/bZIP | |
4 | 109 | 1808 | 1.27E-10 | CACGCG | MYC2-5 | bHLH |
397 | 10,397 | 7.44E-09 | MACGYGB | ABRERATCAL | ABRE | |
469 | 13,792 | 0.000232 | GCCAC | SORLIP1AT | Light | |
137 | 3331 | 0.000652 | ACGTGKC | ACGTABREMOTIFA2OSEM | ABRE | |
286 | 7976 | 0.000884 | WTTSSCSS | E2FCONSENSUS | E2F | |
227 | 6199 | 0.001528 | CACGTG | CACGTGMOTIF | bHLH/bZIP | |
120 | 3057 | 0.005201 | GAGTGAG | SORLIP5AT | Light | |
303 | 8835 | 0.005201 | CTGACY | WBOXNTCHN48 | WRKY | |
5 | 154 | 10,397 | 9.78E-05 | MACGYGB | ABRERATCAL | ABRE |
6 | 131 | 4411 | 1.51E-06 | TGTCGG | ETT-1 | ARF |
149 | 5482 | 1.95E-05 | ACCGAC | DRE2COREZMRAB17 | AP2/ERF | |
185 | 7231 | 1.95E-05 | RCCGAC | DRECRTCOREAT | AP2/ERF | |
285 | 12,862 | 0.000589 | RYCGAC | CBFHV | AP2/ERF | |
325 | 15,123 | 0.000887 | CCWACC | MYBPZM | MYB | |
248 | 11,172 | 0.002184 | ACCWWCC | BOXLCOREDCPAL | MYB | |
128 | 5288 | 0.006668 | TGTCGA | ETT-2 | ARF | |
46 | 1504 | 0.0082 | GGNCCCAC | TCP15 | TCP | |
7 | 67 | 2312 | 0.000349 | GCCGAC | RAP2.3-3 | AP2/ERF |
153 | 7231 | 0.003952 | RCCGAC | DRECRTCOREAT | AP2/ERF | |
116 | 5288 | 0.005831 | TGTCGA | ETT-2 | ARF | |
202 | 10,397 | 0.008081 | MACGYGB | ABRERATCAL | bZIP/bHLH | |
241 | 12,862 | 0.008373 | RYCGAC | CBFHV | AP2/ERF |