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Table 2 Transcription factors with over-represented target motifs in the different clusters

From: From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy

Targets cluster Motif id TF Name Peach genome (v2) gene id TF Cluster Predicted TF family TF Arabidopsis homologous Transcription Factor Predicted function Enrichment adjusted p value
1 - Dark green MP00508 PavAGL15 Prupe.2G023100 7 - red MADS AT5G13790 Agamous-like MADS-box protein AGL15 2.8E-05 (***)
MP00605 PavSEP3 Prupe.1G223600 7 - red MADS AT1G24260 K-box region and MADS-box transcription factor SEP3 / AGL9 2.5E-02 (*)
MP00077 PavAP3 Prupe.1G371300 9 - purple MADS AT3G54340 K-box region and MADS-box transcription factor family protein AP3 2.8E-05 (***)
MP00609 PavAG Prupe.4G070500 9 - purple MADS AT4G18960 K-box region and MADS-box transcription factor AG 2.5E-02 (*)
2 - grey MP00335 PavGATA15 Prupe.1G126000 4 - light blue GATA AT3G06740 GATA transcription factor 15 6.4E-06 (***)
MP00206   Prupe.3G048600 6 - orange C2H2 AT3G13810 Zinc finger protein MAGPIE 7.8E-03 (**)
3 - pink MP00302 PavDREB2C Prupe.2G256900 6 - orange ERF AT2G40340 Dehydration-responsive element-binding protein 2C 3.2E-03 (**)
MP00605 PavSEP3 Prupe.1G223600 7 - red MADS AT1G24260 K-box region and MADS-box transcription factor SEP3 / AGL9 7.4E-03 (**)
4 - light blue MP00527   Prupe.1G480400 4 - light blue ERF AT5G11190 Ethylene-responsive transcription factor 5.0E-04 (***)
MP00394 PavCDF3 Prupe.5G194600 5 - brown Dof AT3G47500 cycling DOF factor 3 3.0E-02 (*)
MP00302 PavDREB2C Prupe.2G256900 6 - orange ERF AT2G40340 Dehydration-responsive element-binding protein 2C 2.7E-03 (**)
MP00508 PavAGL15 Prupe.2G023100 7 - red MADS AT5G13790 Agamous-like MADS-box protein AGL15 1.7E-02 (*)
MP00374 PavERF1 Prupe.1G037900 8 - royal blue ERF AT3G23240 ethylene response factor 1.6E-05 (***)
MP00584   Prupe.6G165700 8 - royal blue ERF AT5G50080 Ethylene-responsive transcription factor 5.2E-03 (**)
MP00315 PavAGL6 Prupe.2G151000 9 - purple MADS AT2G45650 MADS-box transcription factor 2.8E-02 (*)
MP00441   Prupe.4G055600 9 - purple ERF AT4G18450 Ethylene-responsive transcription factor 3.0E-02 (*)
5 - brown MP00527   Prupe.1G480400 4 - light blue ERF AT5G11190 Ethylene-responsive transcription factor 9.6E-08 (***)
MP00302 PavDREB2C Prupe.2G256900 6 - orange ERF AT2G40340 Dehydration-responsive element-binding protein 2C 3.7E-09 (***)
MP00294 PavABI5 Prupe.7G112200 7 - red bZIP AT2G36270 ABSCISIC ACID-INSENSITIVE 5 1.8E-02 (*)
6 - orange MP00402 PavOBP1 Prupe.7G142500 1 - dark green Dof AT3G50410 OBF-binding protein 7.2E-03 (**)
MP00526   Prupe.1G390800 1 - dark green ERF AT5G25190 Ethylene-responsive transcription factor 1.3E-02 (*)
MP00249 PavMYB63 Prupe.4G136300 1 - dark green MYB AT1G79180 myb domain protein 1.3E-02 (*)
7 - red MP00206   Prupe.3G048600 6 - orange C2H2 AT3G13810 Zinc finger protein 2.0E-04 (***)
8 - royal blue MP00526   Prupe.1G390800 1 - dark green ERF AT5G25190 Ethylene-responsive transcription factor 3.6E-02 (*)
MP00581 PavLOB Prupe.5G167800 4 - light blue LBD AT5G63090 Lateral organ boundaries (LOB) domain family protein 2.8E-20 (***)
MP00527 PavSHN3 Prupe.1G480400 4 - light blue ERF AT5G11190 Ethylene-responsive transcription factor 5.9E-03 (**)
MP00624 PavTCX2 Prupe.1G019100 4 - light blue CPP AT4G14770 TESMIN/TSO1-like CXC 2 1.3E-02 (*)
MP00229   Prupe.1G551600 6 - orange C2H2 AT1G72050 transcription factor IIIA 1.1E-02 (*)
MP00302 PavDREB2C Prupe.2G256900 6 - orange ERF AT2G40340 Dehydration-responsive element-binding protein 2C 2.9E-02 (*)
MP00294 PavABI5 Prupe.7G112200 7 - red bZIP AT2G36270 ABSCISIC ACID-INSENSITIVE 5 4.0E-03 (**)
MP00080 PavPI Prupe.1G489400 7 - red MADS AT5G20240 K-box region and MADS-box transcription factor family protein 4.2E-02 (*)
MP00186 PavABF2 Prupe.1G434500 8 - royal blue bZIP AT1G45249 abscisic acid responsive elements-binding factor 0.0E+ 00 (***)
9 - purple MP00375 PavMYB14 Prupe.1G039200 5 - brown MYB AT2G31180 Myb-related protein 7.3E-04 (***)
MP00229   Prupe.1G551600 6 - orange C2H2 AT1G72050 transcription factor IIIA 8.2E-31 (***)
10 - yellow MP00272 PavSVP Prupe.6G199000 1 - dark green MADS AT2G22540 K-box region and MADS-box transcription factor family protein 7.4E-03 (**)
MP00295 PavDOF2 Prupe.6G253300 1 - dark green Dof AT2G37590 Dof zinc finger protein 7.4E-03 (**)
MP00519   Prupe.6G354000 2 - grey ERF AT5G18450 Dehydration-responsive element-binding protein 2G 2.3E-02 (*)
MP00217   Prupe.1G310100 6 - orange ERF AT1G68550 Ethylene-responsive transcription factor 1.7E-02 (*)
MP00374   Prupe.1G037900 8 - royal blue ERF AT3G23240 Ethylene-responsive transcription factor 2.6E-02 (*)
MP00441   Prupe.4G055600 9 - purple ERF AT4G18450 Ethylene-responsive transcription factor 2.6E-02 (*)
  1. We investigated whether some differentially expressed transcription factors specifically targeted motifs in specific clusters. Based on the motif list available for peach was obtained from PlantTFDB [37], overrepresentation of motifs targeted by transcription factors was performed using hypergeometric tests. p-values obtained were corrected using a false discovery rate [38]: (***): adj. p-value <0.001; (**): adj. p-value <0.01; (*): adj. p-value <0.05