Table 4.

Transcription factors found by the combined analysis of transcriptomics and phosphoprotyomics data. With the help of MATCH algorithm we identified overrepresented TF binding sites in promoters of differentially expressed genes (DEG) (from transcriptomics data). TRANSPAC PWM—name of the position weight matrix from TRANSFAC database which was used by MATCH; Yes-No ratio—the ratio of TF site frequency in promoters of DEG compared to the promoters of non-changed genes; p-value—statistical significance of the Yes-No ratio; Phospho Cytoplasm/Nucleus—detection of the phosphorypation of the TF in cytoplasm or in nucleus of the cells (p- phosphorylation was detected, p-up—phosphorylation was found increased upon treatment by RA, p-dn—decreased by RA).

Gene symbol	TF name	TRANSFAC PWM	Yes-No ratio	P-value	UniProt ID	Phospho Cytoplasm	Phospho Nucleus	Gene description
RELA	RelA-p65	V$RELA_Q6	1.22	2.78E-04	Q04206	p	p	v-rel reticuloendotheliosis viral oncogene homolog A (avian)
RXRA	RXR-alpha	V$DR4_Q2	1.34	8.36E-15	P19793	p	p	retinoid X receptor, alpha
SP1	Sp1	V$SP1_Q6_01	2.37	1.36E-85	P08047	p	p-dn	Sp1 transcription factor
CTCF	ctcf	V$CTCF_01	1.71	1.75E-16	P49711	p	p	CCCTC-binding factor (zinc finger protein)
RXRB	RXR-beta	V$DR4_Q2	1.34	8.36E-15	P28702	p	p	retinoid X receptor, beta
TRIM28	RNF96	V$RNF96_01	2.54	6.71E-43	Q13263	p-up	p-dn	tripartite motif containing 28
NFYC	NF-YC	V$NFY_Q3	1.67	1.16E-04	Q13952	p	p	nuclear transcription factor Y, gamma
SP3	Sp3	V$SP1_Q6_01	2.37	1.36E-85	Q02447	p	p	Sp3 transcription factor
RREB1	RREB-1	V$RREB1_01	1.33	1.28E-12	Q92766	p	p-dn	ras responsive element binding protein 1
NR2F2	COUP-TF2	V$DR4_Q2	1.34	8.36E-15	P24468	p	p	nuclear receptor subfamily 2, group F, member 2
KLF4	GKLF	V$GKLF_Q4	1.63	4.06E-135	O43474	p	p-dn	Kruppel-like factor 4 (gut)
PATZ1	PATZ	V$MAZR_01	2.14	1.90E-11	Q9HBE1	p	p	POZ (BTB) and AT hook containing zinc finger 1