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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 clusterMotif idTF NamePeach genome (v2) gene idTF ClusterPredicted TF familyTF Arabidopsis homologousTranscription Factor Predicted functionEnrichment adjusted p value
1 - Dark greenMP00508PavAGL15Prupe.2G0231007 - redMADSAT5G13790Agamous-like MADS-box protein AGL152.8E-05(***)
MP00605PavSEP3Prupe.1G2236007 - redMADSAT1G24260K-box region and MADS-box transcription factor SEP3 / AGL92.5E-02(*)
MP00077PavAP3Prupe.1G3713009 - purpleMADSAT3G54340K-box region and MADS-box transcription factor family protein AP32.8E-05(***)
MP00609PavAGPrupe.4G0705009 - purpleMADSAT4G18960K-box region and MADS-box transcription factor AG2.5E-02(*)
2 - greyMP00335PavGATA15Prupe.1G1260004 - light blueGATAAT3G06740GATA transcription factor 156.4E-06(***)
MP00206 Prupe.3G0486006 - orangeC2H2AT3G13810Zinc finger protein MAGPIE7.8E-03(**)
3 - pinkMP00302PavDREB2CPrupe.2G2569006 - orangeERFAT2G40340Dehydration-responsive element-binding protein 2C3.2E-03(**)
MP00605PavSEP3Prupe.1G2236007 - redMADSAT1G24260K-box region and MADS-box transcription factor SEP3 / AGL97.4E-03(**)
4 - light blueMP00527 Prupe.1G4804004 - light blueERFAT5G11190Ethylene-responsive transcription factor5.0E-04(***)
MP00394PavCDF3Prupe.5G1946005 - brownDofAT3G47500cycling DOF factor 33.0E-02(*)
MP00302PavDREB2CPrupe.2G2569006 - orangeERFAT2G40340Dehydration-responsive element-binding protein 2C2.7E-03(**)
MP00508PavAGL15Prupe.2G0231007 - redMADSAT5G13790Agamous-like MADS-box protein AGL151.7E-02(*)
MP00374PavERF1Prupe.1G0379008 - royal blueERFAT3G23240ethylene response factor1.6E-05(***)
MP00584 Prupe.6G1657008 - royal blueERFAT5G50080Ethylene-responsive transcription factor5.2E-03(**)
MP00315PavAGL6Prupe.2G1510009 - purpleMADSAT2G45650MADS-box transcription factor2.8E-02(*)
MP00441 Prupe.4G0556009 - purpleERFAT4G18450Ethylene-responsive transcription factor3.0E-02(*)
5 - brownMP00527 Prupe.1G4804004 - light blueERFAT5G11190Ethylene-responsive transcription factor9.6E-08(***)
MP00302PavDREB2CPrupe.2G2569006 - orangeERFAT2G40340Dehydration-responsive element-binding protein 2C3.7E-09(***)
MP00294PavABI5Prupe.7G1122007 - redbZIPAT2G36270ABSCISIC ACID-INSENSITIVE 51.8E-02(*)
6 - orangeMP00402PavOBP1Prupe.7G1425001 - dark greenDofAT3G50410OBF-binding protein7.2E-03(**)
MP00526 Prupe.1G3908001 - dark greenERFAT5G25190Ethylene-responsive transcription factor1.3E-02(*)
MP00249PavMYB63Prupe.4G1363001 - dark greenMYBAT1G79180myb domain protein1.3E-02(*)
7 - redMP00206 Prupe.3G0486006 - orangeC2H2AT3G13810Zinc finger protein2.0E-04(***)
8 - royal blueMP00526 Prupe.1G3908001 - dark greenERFAT5G25190Ethylene-responsive transcription factor3.6E-02(*)
MP00581PavLOBPrupe.5G1678004 - light blueLBDAT5G63090Lateral organ boundaries (LOB) domain family protein2.8E-20(***)
MP00527PavSHN3Prupe.1G4804004 - light blueERFAT5G11190Ethylene-responsive transcription factor5.9E-03(**)
MP00624PavTCX2Prupe.1G0191004 - light blueCPPAT4G14770TESMIN/TSO1-like CXC 21.3E-02(*)
MP00229 Prupe.1G5516006 - orangeC2H2AT1G72050transcription factor IIIA1.1E-02(*)
MP00302PavDREB2CPrupe.2G2569006 - orangeERFAT2G40340Dehydration-responsive element-binding protein 2C2.9E-02(*)
MP00294PavABI5Prupe.7G1122007 - redbZIPAT2G36270ABSCISIC ACID-INSENSITIVE 54.0E-03(**)
MP00080PavPIPrupe.1G4894007 - redMADSAT5G20240K-box region and MADS-box transcription factor family protein4.2E-02(*)
MP00186PavABF2Prupe.1G4345008 - royal bluebZIPAT1G45249abscisic acid responsive elements-binding factor0.0E+ 00(***)
9 - purpleMP00375PavMYB14Prupe.1G0392005 - brownMYBAT2G31180Myb-related protein7.3E-04(***)
MP00229 Prupe.1G5516006 - orangeC2H2AT1G72050transcription factor IIIA8.2E-31(***)
10 - yellowMP00272PavSVPPrupe.6G1990001 - dark greenMADSAT2G22540K-box region and MADS-box transcription factor family protein7.4E-03(**)
MP00295PavDOF2Prupe.6G2533001 - dark greenDofAT2G37590Dof zinc finger protein7.4E-03(**)
MP00519 Prupe.6G3540002 - greyERFAT5G18450Dehydration-responsive element-binding protein 2G2.3E-02(*)
MP00217 Prupe.1G3101006 - orangeERFAT1G68550Ethylene-responsive transcription factor1.7E-02(*)
MP00374 Prupe.1G0379008 - royal blueERFAT3G23240Ethylene-responsive transcription factor2.6E-02(*)
MP00441 Prupe.4G0556009 - purpleERFAT4G18450Ethylene-responsive transcription factor2.6E-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