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Table 2 Mapping the universal Cd-responsive DEGs in co-expression network to the metabolic pathways

From: Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes

BinName

Log2Foldchange

Rice gene annotation

Transcript ID

Cd1h

MCd1

MCdD

Cd24h

Stress protein

 Os03g16020.1

4.78

8.93

8.95

6.76

hsp20/alpha crystallin family protein

Abscisic acid synthesis

 Os07g05940.1

5.63

8.61

8.60

7.32

9-cis-epoxycarotenoid dioxygenase, OsNCED4

Jasmonate synthesis and signaling

 Os06g11290.1

5.06

6.25

5.76

4.72

12-oxophytodienoate reductase, OsOPR1

 Os06g11240.1

4.52

5.13

4.38

4.79

OPR

 Os06g11210.1#

3.55

5.19

4.91

3.34

OsOPR5

 Os10g25290.1#

2.72

5.54

4.66

2.97

ZIM domain containing protein, OsJAZ12

 Os03g08330.1

3.36

7.21

6.93

2.02

OsJAZ10

 Os10g25230.1

4.89

7.43

7.38

4.45

OsJAZ13

 Os03g08310.1*

2.99

5.56

4.67

1.86

OsJAZ9

 Os12g05440.1*

4.09

6.83

5.28

4.33

cytochrome P450, CYP94C2b

Ethylene signal transduction

 Os08g36920.1#

5.16

8.29

8.90

5.47

AP2 domain containing protein

 Os07g22730.1

3.17

5.98

7.58

3.40

AP2 domain

 Os09g39850.1

3.71

5.30

5.72

2.72

AP2 domain

 Os09g28440.1

4.67

7.54

7.97

6.41

AP2 domain, OsEATB

 Os02g43790.1

2.57

3.89

4.36

2.09

ethylene-responsive transcription factor, OsBIERF3

 Os05g34730.1

4.99

7.43

8.95

4.88

ethylene-responsive transcription factor, SERF1

Transcription factor family

 Os01g09100.1

2.44

4.65

4.68

3.14

OsWRKY10

 Os01g01870.1

2.53

3.48

1.77

1.58

HLH DNA-binding domain containing protein

 Os01g49160.1

1.91

4.07

3.91

2.11

MYB family transcription factor

 Os01g19330.1

4.33

7.48

7.53

5.03

MYB

 Os02g41510.1#

2.96

4.31

3.82

3.01

MYB

 Os03g60080.1#

3.67

5.08

5.16

3.48

SNAC1

 Os07g12340.1

4.93

6.26

5.91

3.04

OsNAC3

 Os09g31390.1

−1.25

−1.46

−2.64

−1.64

OsbZIP74

Zinc finger proteins

 Os09g21710.1#

2.71

6.17

6.95

2.94

AN1-like zinc finger domain containing protein

 Os03g32230.1#

5.04

7.77

6.03

3.61

ZOS3–12 - C2H2 zinc finger protein

 Os03g60560.1

7.11

9.63

11.52

5.82

ZOS3–21, ZFP182

 Os12g39400.1

2.36

5.08

5.67

2.75

ZOS12–09, ZFP252

 Os03g60570.1

5.12

9.13

8.86

5.79

ZOS3–22

 Os02g45780.1

2.74

5.76

5.24

2.48

zinc finger, C3HC4 type

 Os09g29310.1

3.83

6.05

5.86

2.33

zinc finger, C3HC4 type

Glutathione S transferases

 Os10g22070.1*

2.42

3.04

3.92

2.07

glutathione S-transferase, GST

 Os09g20220.1#

6.43

7.67

7.73

8.32

GST

 Os10g38340.1

6.40

11.52

13.14

7.08

GSTU6

 Os10g38720.1

2.87

5.78

7.45

4.64

GST

 Os03g57200.1

2.10

2.66

2.93

1.35

GST

 Os10g38314.1

5.71

7.11

8.28

5.29

GST

 Os10g38350.1

1.97

3.07

1.94

2.20

GST

ROS regulation-related genes

 Os07g08840.3

5.09

5.39

3.94

4.17

apoplastic H-type thioredoxin, OsTRXh1

 Os04g33390.1*

1.98

3.42

2.26

2.24

prephenate dehydratase / arogenate dehydratase

 Os11g42989.1*

5.09

5.40

6.16

3.81

exo70 exocyst complex subunit

Transporters

 Os01g42380.1#

2.07

4.51

4.56

4.00

ABCG36/OsPDR9

 Os02g37300.1

2.33

4.56

7.04

3.61

HMAD

 Os02g37330.1

4.25

7.19

8.63

4.43

HMAD

 Os03g11900.1

1.15

2.78

2.58

1.99

monosaccharide transporter, OsMST4

others DEGs with Cd-upregulated homologs

 Os02g50730.1

1.90

2.67

3.49

4.41

APK_ORTHOMCL1642, metalloendoproteinase

 Os06g13180.1

3.03

1.88

5.44

5.03

APK_ORTHOMCL1642, metalloendoproteinase

 Os08g04350.1

4.22

4.28

7.54

7.52

APK_ORTHOMCL3089, plastocyanin-like

 Os08g04360.1

4.76

4.90

7.71

8.40

APK_ORTHOMCL3089, plastocyanin-like

 Os08g04370.1

3.04

3.02

5.56

4.75

APK_ORTHOMCL3089, plastocyanin-like

 Os12g18560.1

2.53

3.31

4.95

4.96

APK_ORTHOMCL14694, pectin methylesterase inhibitor

others novel DEGs

 Os01g61990.1*

1.42

1.55

1.15

1.70

ankyrin repeat-containing protein, OsNPR4

 Os03g08520.1*

2.79

4.38

5.32

2.02

DUF581 domain containing protein

 Os03g41330.1*

−1.59

−2.77

−3.08

−1.97

DUF260 domain containing protein

 Os02g25700.1*

−1.31

−2.17

−3.04

−1.23

O-acyltransferase

 Os03g08720.1*

−1.57

−1.75

−3.10

−3.27

transferase family protein

 Os04g43710.1*

−1.23

−2.12

−2.30

−2.63

CAMK, Ca/CaM-depedent protein kinases

 Os06g11030.1*

2.13

4.94

4.84

2.38

EF hand family protein

 Os08g42490.1*

3.47

4.65

7.06

3.91

DC1 domain containing protein

 Os12g43870.1*

3.05

4.39

3.81

3.20

expressed protein

  1. Rice seedling roots samples of medium Cd stress (50 μM) for 1 h and 24 h (designated MCd1 and MCdD, respectively), high Cd pressure (100 μM) for 24 h (labeled as Cd24h) and 1 h (Cd1h, prepared in our lab), and their corresponding control are compared in couples to analyze DEGs using the limma package. The DEGs marked with stars are the uniquely identified DEGs in our RNAseq samples (Cd1h). Those marked with pound signs were also upregulated by medium and low Cd stress in rice seedling roots in 3 previous reports [21, 27, 48], and those with triangle were regulated uniformly by Cd treatments in the two high-throughput studies [21, 27], whereas those labeled M were detected only in the microarray analysis [21]. Those labeled C were general stress-responsive genes that were commonly upregulated by multiple stresses as previously reported [27]. Rice genes with experimentally verified functions are presented in bold fonts, and the homologous DEGs can be categorized into orthologous groups are presented with APK_ORTHOMCL number [86]