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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

From: Combined physiological, transcriptome, and cis-regulatory element analyses indicate that key aspects of ripening, metabolism, and transcriptional program in grapes (Vitis vinifera L.) are differentially modulated accordingly to fruit size

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