Table 2 Differentially expressed genes involved in hormones, Ca2+ signaling, and transcription factor regulation.

From: Functional characterization of maize phytochrome-interacting factor 3 (ZmPIF3) in enhancing salt tolerance in arabidopsis

Gene ID

Gene symbol

Normalized value (FPKM)

Log2 (T1/C1)

FDR (T1/C1)

Log2 (T2/C2)

FDR (T2/C2)

Type

Annotation or Function

C1

T1

C2

T2

Hormone-related

 AT4G36830

HOS3-1

0.677795

6.00271

1.110877

4.898485

2.93612

0.042799

2.22858

0.149163

I

Inhibit abscisic acid(ABA)-mediated stress

 AT5G05440

PYL5

14.3795

56.67855

23.55735

23.0709

1.74533

0.003362

0.048068

0.94698

I

Abscisic acid receptor PYL5

 AT5G45340

CYP707A3

6.59789

4.982175

3.340675

8.07745

−0.60299

0.599182

1.3747

0.0299491

II

Abscisic acid 8'-hydroxylase 3

 AT2G38310

PYL4

25.34465

23.62101

44.76455

5.192435

−0.376158

0.720953

−3.01822

7.14427E−07

II

PYR1-like 4,Receptor for abscisic acid (ABA)

 AT1G33760

 

6.20409

0.312294

1.231961

0.283952

−4.5361

0.010392

−2.05506

0.282947

I

Ethylene-responsive transcription factor ERF022

 AT1G74930

ORA47

16.38577

5.586855

11.43528

25.1818

−1.7431

0.066291

1.21998

0.0369038

II

Ethylene-responsive transcription factor ERF018

 AT5G47230

ERF5

15.8934

53.23745

7.02544

69.7073

1.56989

0.01502

3.37803

4.37383E−12

III

Ethylene-responsive transcription factor 5

 AT5G25190

ESE3

81.8762

14.57868

81.88865

3.60469

−2.75787

0.000164

−4.42434

3.61729E−10

III

Ethylene and salt inducible

 AT1G71520

 

0.070649

110.4826

0.417836

121.8061

10.4691

0.000196

8.26388

1.96722E−11

III

Ethylene-responsive transcription factor ERF020

 AT1G03800

ERF10

0.885593

6.705345

0.310763

8.70786

2.72649

0.026073

4.88305

0.000120489

III

ERF domain protein 10

 AT5G61600

ERF104

24.64325

20.6017

12.63976

43.4625

−0.426433

0.648937

1.86724

0.000276545

II

Ethylene response factor 104

 AT2G47520

ERF71

0.077023

4.16697

0.372978

5.36407

5.6219

0.09321

3.89661

0.0226986

II

Ethylene response factor 71

 AT4G32800

 

11.00635

3.392443

23.30085

1.505988

−1.96191

0.06747

−3.8635

1.08709E−05

II

Ethylene-responsive transcription factor ERF043

 AT3G14230

RAP2.2

51.7091

154.4685

56.83945

187.1145

0

1

1.79421

2.32956E−05

II

Related to AP2 ,Involved in ethylene response

 AT4G31060

 

4.33121

1.102877

6.35298

0.335723

−2.2127

0.175595

−4.18139

0.0232275

II

Ethylene-responsive transcription factor ERF015

 AT3G12955

 

0.363225

2.5588

0.184672

5.135985

2.64684

0.262304

4.89807

0.0353094

II

SAUR-like auxin-responsive family protein

 AT4G36110

SAUR9

11.2771

3.59809

14.7574

0.943365

−1.83537

0.103837

−3.91203

0.00291197

II

SMALL AUXIN UPREGULATED RNA 9

 AT5G10990

 

0.207195

4.99999

0.069728

5.35573

4.42898

0.038084

6.35526

0.0281325

III

SAUR-like auxin-responsive protein

 AT3G15540

IAA19

48.3179

1.54044

45.1675

5.60472

−5.14523

2.42E−06

−2.92945

6.70262E−06

III

Auxin-responsive protein IAA19

 AT4G38860

 

148.5845

2.207505

133.22

0.418762

−6.36668

2.94E−08

−8.21449

1.99262E−08

III

SAUR-like auxin-responsive protein

 AT4G34770

 

23.31555

1.168065

31.24705

0.097227

−4.60908

0.004229

−8.22968

0.00370476

III

SAUR-like auxin-responsive protein

 AT3G03820

SAUR29

38.48575

1.290665

59.0414

0.460642

−5.20135

0.000534

−6.9049

3.50106E−05

III

SMALL AUXIN UP RNA 29

 AT5G12050

 

87.6732

0.704796

77.8011

0.111487

−7.22296

8.59E−10

−9.364

1.71E−08

III

Involved in auxin transport

 AT4G14550

IAA14

15.4711

0.397462

14.1758

0.03277

−5.3887

0.041134

−8.6602

0.0181967

III

Auxin-responsive protein IAA14

 AT1G77690

LAX3

4.36963

1.135613

4.53357

0.236858

−2.19993

0.08015

−4.16564

0.00194242

II

Involved in proton-driven auxin influx

 AT4G36540

BEE2

27.84305

0.389752

24.38715

0.043393

−6.45158

0.000371

−9.0309

0.0926954

I

BR enhanced expression 2

 AT1G18400

BEE1

18.64985

0.434204

19.31685

0.124071

−5.72154

0.006202

−7.22585

0.00949789

III

BR enhanced expression 1

 AT4G08950

EXO

27.39865

25.07557

30.5728

7.3498

−0.387449

0.712905

−1.96781

0.00225442

II

May mediate BR-induced leaf growth

 AT1G04240

SHY2

32.0148

2.647326

42.1678

0.612936

−3.89313

0.009082

−6.0797

0.011564

III

AUX/IAA transcriptional regulator family protein

 AT5G56650

ILL1

10.9704

3.505705

14.0197

1.053307

−1.91396

0.097894

−3.66703

5.70461E−05

II

IAA-leucine resistant (ILR)-like 1

 AT5G13220

JAZ10

4.880135

25.7823

15.57092

23.3146

2.21848

0.018758

0.640391

0.360252

I

Response to salicylic acid or indole-3-acetic acid

 AT3G16470

JR1

209.2042

91.82775

507.1075

40.1118

−1.42646

0.158117

−3.58201

4.88085E−13

II

JA-responsive gene

Ca2 + signaling

 AT1G66400

CML23

8.141395

63.2669

4.40952

116.0337

2.77829

1.71E−05

4.79657

0

III

Calmodulin like 23; Potential calcium sensor

 AT3G50770

CML41

26.3997

44.0276

57.8481

15.46115

0.51274

0.555663

−1.82066

0.001179

II

Calmodulin-like 41

 AT5G42380

CML37

5.718575

133.892

4.842385

276.7335

4.39087

9.87E−13

5.90073

0

III

Calmodulin like 37

 AT4G17615

CBL1

2.035335

12.8309

2.616875

15.76645

2.49061

0.104286

2.66743

0.010816

II

Calcineurin B-like protein 1

 AT1G76640

 

3.17538

0.632561

13.32017

0.254006

−2.50128

0.255479

−5.62238

0.018306

II

Calcium-binding protein CML39

 AT3G47480

 

9.31846

4.741715

19.4546

2.039417

−1.20936

0.308717

−3.16031

0.000683

II

Calcium-binding EF-hand family protein

 AT3G16510

 

3.992

12.50445

2.94993

23.43685

1.46361

0.081453

3.06024

1.4E−07

II

Calcium-dependent domain-containing protein

 AT5G23950

 

0.1801015

32.218

1.377265

32.56975

7.28185

0.001568

4.65204

2.39E−08

III

Calcium-dependent domain-containing protein

 AT4G00700

 

0.1167728

6.85807

0.518394

8.59376

5.69153

0.000159

4.13256

2.18E−08

III

C2 calcium/lipid-binding family protein

 AT3G29000

 

6.562985

78.7937

2.710275

111.005

3.40844

3.3E−07

5.43101

0

III

Calcium-binding EF-hand family protein

Transcription factors

 AT5G61420

MYB28

14.998

1.065375

15.58165

0.221147

−4.11357

0.022849

−6.04544

8.9E−05

III

MYB domain protein 28

 AT3G50060

MYB77

25.14165

8.183985

19.6408

18.21507

−1.8409

0.011836

−0.02455

0.975555

I

MYB domain protein 77

 AT5G54230

MYB49

0.532255

4.447695

0.120885

4.796465

2.90713

0.056126

5.38925

0.002174

II

MYB domain protein 49

 AT1G48000

MYB112

0.393105

27.68795

1.666525

30.8896

5.98296

0.000178

4.28998

5.35E−08

III

MYB domain protein 112

 AT5G61600

ERF104

24.64325

20.6017

12.63976

43.4625

−0.42643

0.648937

1.86724

0.000277

II

Ethylene response transcription factor 104

 AT2G47520

ERF71

0.077023

4.16697

0.372978

5.36407

5.6219

0.09321

3.89661

0.022699

II

Ethylene response transcription factor 71

 AT5G47230

ERF5

15.8934

53.23745

7.02544

69.7073

1.56989

0.01502

3.37803

4.37E−12

III

Ethylene-responsive transcription factor 5

 AT1G03800

ERF10

0.885593

6.705345

0.310763

8.70786

2.72649

0.026073

4.88305

0.00012

III

ERF domain protein 10

 AT5G51990

CBF4

0.439356

5.364015

0.062366

20.09175

3.47437

0.058829

8.42832

0.002083

II

C-repeat-binding factor 4

 AT4G25490

CBF1

1.720604

1.946955

0.139687

5.6805

0.040821

0.989044

5.42484

0.004792

II

C-repeat/DRE binding factor 1

 AT4G25470

CBF2

9.110715

4.989725

1.719745

10.31723

−1.05739

0.383755

2.66504

0.002557

II

C-repeat/DRE binding factor 2

 AT5G65640

bHLH093

7.598545

5.143727

8.15712

0.802256

−0.82407

0.578874

−3.28036

0.005542

II

Beta HLH protein 93

 AT1G22490

 

0.47868

5.87791

0.845117

2.772765

3.39527

0.021123

1.79016

0.242383

I

Transcription factor bHLH94

 AT5G15830

bZIP3

5.731815

1.34438

6.255265

0.177588

−2.37087

0.108926

−5.07688

0.012851

II

Basic leucine-zipper 3

 AT4G31800

WRKY18

8.883715

162.871

27.71205

119.722

4.00959

2.34E−10

2.18392

2.22E−06

III

WRKY DNA-binding protein 18

  1. C1: WT seedling under normal condition; C2: overexpressed transgenic seedling under normal condition; T1: WT seedling treated by salt stress; T2: overexpressed transgenic seedling treated by salt stress.
  2. This table lists genes differentially expressed in response to salt stress, categorized by their involvement in hormonal pathways, calcium signaling, and transcription factor regulation. Each gene is identified by its gene ID and symbol, with normalized expression values provided for both control (C) and treated (T) conditions at 4 days (4d). Expression levels are represented as normalized values (FPKM) and the log2 ratios between treated and control conditions for both WT and transgenic Arabidopsis, indicating the fold change due to salt stress. False discovery rates (FDR) are given to indicate the statistical significance of the differential expression. The ‘Type’ column categorizes genes by their functional annotation, providing insight into the potential roles these genes may play in stress response mechanisms.
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