Table 1.

List of 28 master regulators that control geraniol‐specific cell cycle signatures

Gene ID	Gene symbol	Gene description	FET P ‐Valuea	Markers in regulonb	Markers in intersection setc	Moded	Odds Ratioe	NESf	absNES	Fold Changeg	q‐valueg
79733	E2F8	E2F transcription factor 8	3.31E‐43	478	58	—	15.00	−13.72	13.72	0.66	0.00
4605	MYBL2	v‐myb myeloblastosis viral oncogene homolog‐like 2	9.02E‐30	539	50	—	15.77	−13.79	13.79	0.68	0.00
2146	EZH2	Enhancer of zeste homolog 2 (Drosophila)	7.32E‐24	578	46	—	12.25	−14.68	14.68	0.73	0.00
1063t	CENPF	Centromere protein F, 350/400 kDa (mitosin)	1.75E‐21	493	41	—	16.32	−12.51	12.51	0.56	0.00
3148	HMGB2	High mobility group box 2	3.34E‐20	501	40	—	8.74	−12.44	12.44	0.63	0.00
3149t	HMGB3	High mobility group box 3	6.28E‐24	400	40	—	16.41	−11.34	11.34	0.75	0.00
8914	TIMELESS	Timeless homolog (Drosophila)	1.04E‐21	457	40	—	10.64	−12.38	12.38	0.83	0.00
865	CBFB	Core‐binding factor, beta subunit	8.91E‐15	597	37	—	9.97	−13.25	13.25	0.85	0.01
8607	RUVBL1	RuvB‐like 1 (E. coli)	1.29E‐11	751	37	—	9.14	−13.41	13.41	0.73	0.00
11137	PWP1	PWP1 homolog (S. cerevisiae)	1.47E‐14	571	36	—	6.98	−12.81	12.81	0.90	0.24
2305	FOXM1	Forkhead box M1	2.07E‐15	504	35	—	11.99	−13.21	13.21	0.69	0.00
9232	PTTG1	Pituitary tumor‐transforming 1	2.52E‐15	475	34	—	10.12	−12.19	12.19	0.54	0.00
4602	MYB	v‐myb myeloblastosis viral oncogene homolog	4.96E‐14	524	34	—	11.80	−11.35	11.35	0.62	0.00
7468	WHSC1	Wolf‐Hirschhorn syndrome candidate 1	9.73E‐12	590	33	—	9.17	−13.29	13.29	0.77	0.00
9735	KNTC1	Kinetochore associated 1	2.44E‐16	354	31	—	10.77	−10.71	10.71	0.70	0.00
10856	RUVBL2	RuvB‐like 2 (E. coli)	4.11E‐12	502	31	—	8.55	−11.67	11.67	0.83	0.00
4603	MYBL1	v‐myb myeloblastosis viral oncogene homolog‐like 1	4.01E‐14	336	28	—	11.84	−10.73	10.73	0.76	0.00
2130	EWSR1	Ewing sarcoma breakpoint region 1	5.32E‐13	372	28	—	12.31	−8.79	8.79	0.82	0.00
5252	PHF1	PHD finger protein 1	1.46E‐10	468	28	+	7.60	11.45	11.45	1.16	0.02
10849	CD3EAP	CD3e molecule, epsilon‐associated protein	3.76E‐11	378	26	—	17.60	−11.50	11.50	0.79	0.00
221037	JMJD1C	Jumonji domain containing 1C	1.08E‐08	453	25	+	19.28	9.36	9.36	1.32	0.00
7020	TFAP2A	Transcription factor AP‐2 alpha	4.85E‐10	359	24	+	5.16	6.01	6.01	1.23	0.00
10042	HMGXB4	HMG box domain containing 4	1.86E‐05	582	23	—	7.59	−10.37	10.37	0.76	0.00
5036	PA2G4	Proliferation‐associated 2G4, 38 kDa	2.06E‐08	364	22	—	14.26	−11.18	11.18	0.82	0.00
9569	GTF2IRD1	GTF2I repeat domain containing 1	1.07E‐07	331	20	+	6.67	7.26	7.26	1.19	0.01
7027	TFDP1	Transcription factor Dp‐1	2.12E‐06	398	20	—	15.56	−11.73	11.73	0.70	0.00
86	ACTL6A	Actin‐like 6A	1.55E‐06	287	17	—	7.17	−3.26	3.26	0.76	0.00
25909	AHCTF1	AT hook containing transcription factor 1	1.96E‐05	346	17	—	7.02	−8.44	8.44	0.83	0.01

The 28 MRs were sorted by largest to smallest by Markers in intersection set in descendent order. Odds ratio, NES, fold change and q‐value were rounded off to two decimal places.

^aFET P ‐value, the P ‐value from Fisher's exact test. It shows how much significantly the marker (gene) belongs to the signature set and the regulon of the master regulator (MR).

^bMarkers in regulon, the number of markers (genes) found to be first neighbors of the master regulator in the loaded network.

^cMakers in intersection set, the number of markers found in the intersection of the signature and the regulon of the candidate MR.

^dMode, plus mode means that the MR is positively correlated with up‐regulated regulons in geraniol cluster, and minus mode means that the MR is positively correlated with down‐regulated genes in geraniol cluster.

^eOdd Ratio, odds of a regulon gene being in the GSEA leading edge set/odds of a regulon gene being in the GSEA trailing edge set.

^fNES, GSEA normalized enrichment score for the regulon of the TF.

^gFold change and q‐value were calculated from SAM analysis.