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

Table 1 Transcription factors with over-represented targets in the different clusters

Targets cluster	TF Name	Peach genome (v2) gene id	TF Cluster	Predicted TF family	TF Arabidopsis homologous	TF Predicted function	Enrichment adjusted p value
1 - dark green	PavMYB63	Prupe.4G136300	1 - dark green	MYB	AT1G79180	Myb-related protein	6.7E-03	(**)
	PavMYB93	Prupe.6G188300	1 - dark green	MYB	AT1G34670	Myb-related protein	3.2E-02	(*)
	PavMYB40	Prupe.3G299000	8 - royal blue	MYB	AT5G14340	Myb-related protein	1.7E-02	(*)
3 - pink	PavWRKY40	Prupe.3G098100	3 - pink	WRKY	AT1G80840	WRKY transcription factor	1.2E-02	(*)
6 - orange	PavERF110	Prupe.6G165700	8 - royal blue	ERF	AT5G50080	Ethylene-responsive transcription factor	5.2E-02
6 - orange	PavRVE8	Prupe.6G242700	8 - royal blue	MYB	AT3G09600	Homeodomain-like superfamily protein RVE8	5.2E-02
8 - royal blue	PavRVE1	Prupe.3G014900	6 - orange	MYB	AT5G17300	Homeodomain-like superfamily protein RVE1	3.6E-02	(*)
	PavABI5	Prupe.7G112200	7 - red	bZIP	AT2G36270	ABSCISIC ACID-INSENSITIVE 5	7.0E-03	(**)
	PavABF2	Prupe.1G434500	8 - royal blue	bZIP	AT1G45249	abscisic acid responsive elements-binding factor	7.5E-04	(***)
10 - yellow	PavMYB14	Prupe.1G039200	5 - brown	MYB	AT2G31180	Myb-related protein	3.9E-02	(*)

We investigated whether some differentially expressed transcription factors specifically targeted genes in specific clusters. Based on the gene regulation information available for peach in PlantTFDB [37], overrepresentation of genes targeted by transcription factors was performed using hypergeometric tests. p-values obtained were corrected using a false discovery rate: (***): adj. p-value <0.001; (**): adj. p-value <0.01; (*): adj. p-value <0.05

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