Table 2. Gene expression during plant regeneration in Auxin.

Description	Gene-id	Regenerating callus vs Callus_Read_count	Cyclohexane vs Callus_Read_count	Callus_Read_count	Regenerating callus vs Callus_log2 Fold Change	Cyclohexane vs Callus_log2 Fold Change	pval	padj
auxin-responsive protein IAA	Cluster-6172.2761	25.79	/	291.87	-3.5	/	1.53E-20	7.20E-19
auxin-responsive protein IAA	Cluster-6172.9506	1350.90	/	7436.54	-2.46	/	8.50E-33	1.36E-30
auxin-responsive protein IAA	Cluster-6172.9484	3097.05	/	8093.56	-1.39	/	9.12E-09	8.99E-08
auxin-responsive protein IAA	Cluster-6172.6741	115.19	/	752.97	-2.72	/	4.06E-30	5.09E-28
auxin-responsive protein IAA	Cluster-6172.4574	329.74	/	2581.01	-2.97	/	5.94E-28	5.78E-26
auxin-responsive protein IAA	Cluster-7966.13997	/	126.90	427.80	/	-1.76	1.96E-13	1.49E-12
auxin-responsive protein IAA	Cluster-7966.10326	/	2912.32	6803.46	/	-1.22	1.54E-20	1.99E-19
auxin-responsive protein IAA	Cluster-7966.9984	/	757.43	2282.82	/	-1.59	5.19E-39	2.10E-37
auxin-responsive protein IAA	Cluster-7966.7990	/	882.15	7136.37	/	-3.02	1.35E-109	9.48E-107
auxin-responsive protein IAA	Cluster-7966.3823	/	24.87	135.71	/	-2.45	3.10E-16	2.89E-15
auxin-responsive protein IAA	Cluster-7966.9412	/	68.99	688.29	/	-3.32	1.37E-77	3.22E-75
auxin-responsive protein IAA	Cluster-7966.8499	/	2134.92	8945.72	/	-2.07	4.70E-93	1.83E-90
auxin response factor	Cluster-6172.11643	642.33	/	5159.89	-3.01	/	1.02E-27	9.71E-26
auxin response factor	Cluster-7966.6357	/	821.41	2005.68	/	-1.29	1.79E-22	2.67E-21
auxin response factor	Cluster-7966.4925	/	2164.10	4677.23	/	-1.11	8.03E-30	1.93E-28
auxin-responsive GH3 gene family	Cluster-6172.10088	766.11	/	5210.20	-2.77	/	7.72E-22	4.27E-20
auxin-responsive GH3 gene family	Cluster-7966.4925	/	2164.10	4677.23	/	-1.11	8.03E-30	1.93E-28
SAUR family protein	Cluster-6172.1833	1482.63	/	191.08	2.96	/	1.56E-18	5.86E-17
SAUR family protein	Cluster-6172.15713	151.85	/	76.04	1	/	0.0052791	0.017525
SAUR family protein	Cluster-2913.0	88.15	/	25.02	1.82	/	1.24E-05	7.06E-05
SAUR family protein	Cluster-3967.0	0.34	/	9.71	-4.74	/	0.0020559	0.007526
SAUR family protein	Cluster-6172.19466	95.93	/	263.01	-1.45	/	0.00046131	0.0019407
SAUR family protein	Cluster-6172.1791	33.88	/	139.87	-2.06	/	1.44E-09	1.61E-08
SAUR family protein	Cluster-6172.18366	200.57	/	541.46	-1.43	/	3.18E-08	2.84E-07
SAUR family protein	Cluster-6172.17182	61.02	/	123.87	-1.03	/	0.0078308	0.024821
SAUR family protein	Cluster-6172.17013	11.05	/	235.41	-4.44	/	6.48E-30	7.95E-28
SAUR family protein	Cluster-5374.0	11.48	/	33.53	-1.52	/	0.016176	0.046631
SAUR family protein	Cluster-6172.13654	51.66	/	993.51	-4.26	/	8.32E-34	1.46E-31
SAUR family protein	Cluster-1875.0	/	191.22	56.28	/	1.77	1.48E-12	1.04E-11
SAUR family protein	Cluster-7966.1555	/	9.76	60.96	/	-2.64	4.36E-07	1.89E-06
SAUR family protein	Cluster-3489.0	/	26.37	109.08	/	-2.05	1.81E-11	1.17E-10
SAUR family protein	Cluster-7372.0	/	50.62	235.25	/	-2.21	5.44E-15	4.64E-14
SAUR family protein	Cluster-7966.7594	/	163.41	768.46	/	-2.24	2.29E-31	6.09E-30
SAUR family protein	Cluster-7966.11015	/	217.56	523.54	/	-1.27	5.94E-18	6.34E-17
SAUR family protein	Cluster-7966.4605	/	222.98	490.60	/	-1.14	7.22E-07	3.04E-06
SAUR family protein	Cluster-7966.15997	/	23.92	206.53	/	-3.12	4.05E-27	8.18E-26
SAUR family protein	Cluster-7966.11607	/	88.77	876.28	/	-3.31	1.04E-55	9.68E-54
Ethylene-responsive transcription factor 3	Cluster-6172.9509	96.48	/	1004.22	-3.38	/	1.88E-29	2.15E-27
Ethylene-responsive transcription factor 3	Cluster-6172.14530	97.26	/	1695.50	-4.12	/	1.27E-35	2.68E-33
cysteine-rich receptor	Cluster-6172.505	11.82	/	80.91	-2.77	/	1.41E-06	9.59E-06
Zinc finger	Cluster-6172.2152	66.61	/	133.41	-1	/	0.011746	0.035246
Zinc finger	Cluster-6172.19271	48.99	/	12.35	2	/	0.00093637	0.0036929
Zinc finger	Cluster-2307.0	24.64	/	90.13	-1.86	/	0.00013142	0.0006126
Zinc finger	Cluster-2857.0	1.30	/	11.91	-3.17	/	0.0031694	0.011129