Table 2. Open in new tab Transcription...

		All	Upregulated	Downregulated
AT3G20770	EIN3	2.34	0.00	2.98	0.00	0.67	0.46
AT5G11510	MYB3R4	1.54	0.00	1.35	0.08	1.74	0.00
AT5G63090	LOB	1.35	0.01	1.12	0.22	1.59	0.03
AT5G65130	AP2-EREBP	1.21	0.00	1.08	0.19	1.36	0.03
AT1G46768	RAP2.1	1.17	0.00	1.10	0.16	1.24	0.04
AT1G01250	AP2-EREBP	1.74	0.00	1.73	0.12	1.74	0.07
AT5G47230	ERF5	1.53	0.02	1.40	0.22	1.67	0.08
AT5G62020	HSFB2A	1.13	0.05	1.23	0.20	1.02	0.21
AT2G41690	HSFB3	1.13	0.05	1.42	0.12	0.69	0.46
AT5G13910	LEP, LET	1.69	0.02	0.56	0.70	2.42	0.01
AT4G27950	CRF4	1.23	0.00	0.75	0.35	1.66	0.00
AT1G43700	VIP1	1.07	0.03	0.62	0.59	1.48	0.03
AT3G10030	None	1.03	0.01	0.90	0.24	1.17	0.04
AT1G44830	AP2-EREBP	1.11	0.02	0.88	0.34	1.35	0.06
AT3G23220	AP2-EREBP	1.07	0.03	0.94	0.32	1.21	0.10
AT5G02320	MYB3R5	0.99	0.01	0.51	0.59	1.42	0.01
AT1G03800	ERF10	0.99	0.00	0.82	0.12	1.17	0.00
AT2G30340	LOB13	0.92	0.01	0.69	0.27	1.15	0.02
AT1G70920	HB18	0.90	0.00	0.64	0.27	1.16	0.01
AT5G18560	PUCHI	0.88	0.03	0.46	0.60	1.27	0.02
AT1G50640	ERF3	0.86	0.02	-0.27	0.98	1.59	0.00
AT4G34410	RRTF1	0.85	0.00	0.54	0.32	1.15	0.00
AT5G23930	MTERF34	0.82	0.00	0.40	0.51	1.20	0.00
AT1G53910	RAP2.12	0.81	0.00	0.52	0.30	1.10	0.00
AT1G43160	RAP2.6	0.64	0.01	0.22	0.78	1.03	0.00

All

Upregulated

Downregulated

Gene ID

Primary gene name/family

logFC

adj.pval

logFC

adj.pval

logFC

adj.pval

AT3G20770

EIN3

2.34

0.00

2.98

0.00

0.67

0.46

AT5G11510

MYB3R4

1.54

0.00

1.35

0.08

1.74

0.00

AT5G63090

LOB

1.35

0.01

1.12

0.22

1.59

0.03

AT5G65130

AP2-EREBP

1.21

0.00

1.08

0.19

1.36

0.03

AT1G46768

RAP2.1

1.17

0.00

1.10

0.16

1.24

0.04

AT1G01250

AP2-EREBP

1.74

0.00

1.73

0.12

1.74

0.07

AT5G47230

ERF5

1.53

0.02

1.40

0.22

1.67

0.08

AT5G62020

HSFB2A

1.13

0.05

1.23

0.20

1.02

0.21

AT2G41690

HSFB3

1.13

0.05

1.42

0.12

0.69

0.46

AT5G13910

LEP, LET

1.69

0.02

0.56

0.70

2.42

0.01

AT4G27950

CRF4

1.23

0.00

0.75

0.35

1.66

0.00

AT1G43700

VIP1

1.07

0.03

0.62

0.59

1.48

0.03

AT3G10030

None

1.03

0.01

0.90

0.24

1.17

0.04

AT1G44830

AP2-EREBP

1.11

0.02

0.88

0.34

1.35

0.06

AT3G23220

AP2-EREBP

1.07

0.03

0.94

0.32

1.21

0.10

AT5G02320

MYB3R5

0.99

0.01

0.51

0.59

1.42

0.01

AT1G03800

ERF10

0.99

0.00

0.82

0.12

1.17

0.00

AT2G30340

LOB13

0.92

0.01

0.69

0.27

1.15

0.02

AT1G70920

HB18

0.90

0.00

0.64

0.27

1.16

0.01

AT5G18560

PUCHI

0.88

0.03

0.46

0.60

1.27

0.02

AT1G50640

ERF3

0.86

0.02

-0.27

0.98

1.59

0.00

AT4G34410

RRTF1

0.85

0.00

0.54

0.32

1.15

0.00

AT5G23930

MTERF34

0.82

0.00

0.40

0.51

1.20

0.00

AT1G53910

RAP2.12

0.81

0.00

0.52

0.30

1.10

0.00

AT1G43160

RAP2.6

0.64

0.01

0.22

0.78

1.03

0.00

		All	Upregulated	Downregulated
AT3G20770	EIN3	2.34	0.00	2.98	0.00	0.67	0.46
AT5G11510	MYB3R4	1.54	0.00	1.35	0.08	1.74	0.00
AT5G63090	LOB	1.35	0.01	1.12	0.22	1.59	0.03
AT5G65130	AP2-EREBP	1.21	0.00	1.08	0.19	1.36	0.03
AT1G46768	RAP2.1	1.17	0.00	1.10	0.16	1.24	0.04
AT1G01250	AP2-EREBP	1.74	0.00	1.73	0.12	1.74	0.07
AT5G47230	ERF5	1.53	0.02	1.40	0.22	1.67	0.08
AT5G62020	HSFB2A	1.13	0.05	1.23	0.20	1.02	0.21
AT2G41690	HSFB3	1.13	0.05	1.42	0.12	0.69	0.46
AT5G13910	LEP, LET	1.69	0.02	0.56	0.70	2.42	0.01
AT4G27950	CRF4	1.23	0.00	0.75	0.35	1.66	0.00
AT1G43700	VIP1	1.07	0.03	0.62	0.59	1.48	0.03
AT3G10030	None	1.03	0.01	0.90	0.24	1.17	0.04
AT1G44830	AP2-EREBP	1.11	0.02	0.88	0.34	1.35	0.06
AT3G23220	AP2-EREBP	1.07	0.03	0.94	0.32	1.21	0.10
AT5G02320	MYB3R5	0.99	0.01	0.51	0.59	1.42	0.01
AT1G03800	ERF10	0.99	0.00	0.82	0.12	1.17	0.00
AT2G30340	LOB13	0.92	0.01	0.69	0.27	1.15	0.02
AT1G70920	HB18	0.90	0.00	0.64	0.27	1.16	0.01
AT5G18560	PUCHI	0.88	0.03	0.46	0.60	1.27	0.02
AT1G50640	ERF3	0.86	0.02	-0.27	0.98	1.59	0.00
AT4G34410	RRTF1	0.85	0.00	0.54	0.32	1.15	0.00
AT5G23930	MTERF34	0.82	0.00	0.40	0.51	1.20	0.00
AT1G53910	RAP2.12	0.81	0.00	0.52	0.30	1.10	0.00
AT1G43160	RAP2.6	0.64	0.01	0.22	0.78	1.03	0.00

Table 2.

Open in new tab

Transcription factors enriched in ethylene root ‘gold standard’ genes. Transcription factors which are enriched with a P < 0.05 and logFC > 1 in at least one of these groups: all gold standard genes (as defined in Harkey et al. 2019), upregulated gold standard genes or downregulated gold standard genes. TF family name is in italics where gene name was not available.

		All		Upregulated		Downregulated
Gene ID	Primary gene name/family	logFC	adj.pval	logFC	adj.pval	logFC	adj.pval
AT3G20770	EIN3	2.34	0.00	2.98	0.00	0.67	0.46
AT5G11510	MYB3R4	1.54	0.00	1.35	0.08	1.74	0.00
AT5G63090	LOB	1.35	0.01	1.12	0.22	1.59	0.03
AT5G65130	AP2-EREBP	1.21	0.00	1.08	0.19	1.36	0.03
AT1G46768	RAP2.1	1.17	0.00	1.10	0.16	1.24	0.04
AT1G01250	AP2-EREBP	1.74	0.00	1.73	0.12	1.74	0.07
AT5G47230	ERF5	1.53	0.02	1.40	0.22	1.67	0.08
AT5G62020	HSFB2A	1.13	0.05	1.23	0.20	1.02	0.21
AT2G41690	HSFB3	1.13	0.05	1.42	0.12	0.69	0.46
AT5G13910	LEP, LET	1.69	0.02	0.56	0.70	2.42	0.01
AT4G27950	CRF4	1.23	0.00	0.75	0.35	1.66	0.00
AT1G43700	VIP1	1.07	0.03	0.62	0.59	1.48	0.03
AT3G10030	None	1.03	0.01	0.90	0.24	1.17	0.04
AT1G44830	AP2-EREBP	1.11	0.02	0.88	0.34	1.35	0.06
AT3G23220	AP2-EREBP	1.07	0.03	0.94	0.32	1.21	0.10
AT5G02320	MYB3R5	0.99	0.01	0.51	0.59	1.42	0.01
AT1G03800	ERF10	0.99	0.00	0.82	0.12	1.17	0.00
AT2G30340	LOB13	0.92	0.01	0.69	0.27	1.15	0.02
AT1G70920	HB18	0.90	0.00	0.64	0.27	1.16	0.01
AT5G18560	PUCHI	0.88	0.03	0.46	0.60	1.27	0.02
AT1G50640	ERF3	0.86	0.02	-0.27	0.98	1.59	0.00
AT4G34410	RRTF1	0.85	0.00	0.54	0.32	1.15	0.00
AT5G23930	MTERF34	0.82	0.00	0.40	0.51	1.20	0.00
AT1G53910	RAP2.12	0.81	0.00	0.52	0.30	1.10	0.00
AT1G43160	RAP2.6	0.64	0.01	0.22	0.78	1.03	0.00

		All		Upregulated		Downregulated
Gene ID	Primary gene name/family	logFC	adj.pval	logFC	adj.pval	logFC	adj.pval
AT3G20770	EIN3	2.34	0.00	2.98	0.00	0.67	0.46
AT5G11510	MYB3R4	1.54	0.00	1.35	0.08	1.74	0.00
AT5G63090	LOB	1.35	0.01	1.12	0.22	1.59	0.03
AT5G65130	AP2-EREBP	1.21	0.00	1.08	0.19	1.36	0.03
AT1G46768	RAP2.1	1.17	0.00	1.10	0.16	1.24	0.04
AT1G01250	AP2-EREBP	1.74	0.00	1.73	0.12	1.74	0.07
AT5G47230	ERF5	1.53	0.02	1.40	0.22	1.67	0.08
AT5G62020	HSFB2A	1.13	0.05	1.23	0.20	1.02	0.21
AT2G41690	HSFB3	1.13	0.05	1.42	0.12	0.69	0.46
AT5G13910	LEP, LET	1.69	0.02	0.56	0.70	2.42	0.01
AT4G27950	CRF4	1.23	0.00	0.75	0.35	1.66	0.00
AT1G43700	VIP1	1.07	0.03	0.62	0.59	1.48	0.03
AT3G10030	None	1.03	0.01	0.90	0.24	1.17	0.04
AT1G44830	AP2-EREBP	1.11	0.02	0.88	0.34	1.35	0.06
AT3G23220	AP2-EREBP	1.07	0.03	0.94	0.32	1.21	0.10
AT5G02320	MYB3R5	0.99	0.01	0.51	0.59	1.42	0.01
AT1G03800	ERF10	0.99	0.00	0.82	0.12	1.17	0.00
AT2G30340	LOB13	0.92	0.01	0.69	0.27	1.15	0.02
AT1G70920	HB18	0.90	0.00	0.64	0.27	1.16	0.01
AT5G18560	PUCHI	0.88	0.03	0.46	0.60	1.27	0.02
AT1G50640	ERF3	0.86	0.02	-0.27	0.98	1.59	0.00
AT4G34410	RRTF1	0.85	0.00	0.54	0.32	1.15	0.00
AT5G23930	MTERF34	0.82	0.00	0.40	0.51	1.20	0.00
AT1G53910	RAP2.12	0.81	0.00	0.52	0.30	1.10	0.00
AT1G43160	RAP2.6	0.64	0.01	0.22	0.78	1.03	0.00

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