Rice (Oryza sativa L.) is one of the most important staple foods in the world. Therefore, the identification genetic variants associated with improvements in grain yield would facilitate the breeding of new high-yielding rice varieties. Use current knowledge to identify rice yield-related genes with network prediction methods. We proposed a computational systems biology approach for the identification of candidate genes via a random walk model on a PPI network with functional similarities. Starting from known nodes, a random walker travels to its neighbors or jumps to itself in the network, scores a gene using the probability that the walker stays in the gene at a steady state, and then ranks candidate genes according to their scores. We demonstrated the high performance of this approach by a five-fold cross-validation experiment, as well as the robustness of the parameter r. We also assessed the strength of associations between known seeds and candidate genes in the light of the results scores. The candidates ranking at the top of the results list were considered to be the most relevant rice yield-related genes. The prioritization of candidate genes is publicly released to facilitate future discovery of rice yield-related genes.

 

 

 

The predicted genetic landscape of rice yield

Data

Description

Format

Download

Prioritization results

In the functional similarity network, all candidate genes were prioritized by RWR according to vector P at the final status. Each line contains ranking of the corresponding gene as well as the P score.

xlsx

Functional interaction network

The background network comes from the STRING database because of existing potential associated interactions among the proteins. Functional similarities among genes in the background network were considered by scoring edges for Gene Ontology annotations. The network composes of 6561 nodes and 567034 edges.

txt

Gene Ontology

We obtained functional annotation information from the GO Consortium, and downloaded GO annotations of Oryza sativa from the most recent GO version.

gaf

Cross validation

The matching numbers of the five-part seed genes were applied to assess the effectiveness of RWR. The number of matched seeds among the top 500 in the ranking list shown the parameter r=0.3 was was higher than the other r values.

rar

Script

The  programming language is perl and R, using these scripts to achieving the results

rar

 

 

 

The top 100 candidate genes in the ranking list with score and literature validation.

 

rank

name

score

PubMedID

rank

name

score

PubMedID

1

LOC_Os06g09390

0.001487617

PMID: 20713616, PMID: 27555860

51

LOC_Os01g14830

0.000454589

 

2

LOC_Os06g50480

0.001475286

52

LOC_Os01g10820

0.000453601

 

3

LOC_Os02g02480

0.00146746

53

LOC_Os10g42110

0.000449388

 

4

LOC_Os08g42470

0.001461294

54

LOC_Os03g26860

0.000448345

 

5

LOC_Os01g03340

0.000941415

55

LOC_Os07g41750

0.000448221

 

6

LOC_Os01g03390

0.00080268

PMID: 12972663

56

LOC_Os03g17580

0.000448145

 

7

LOC_Os01g04040

0.00080268

57

LOC_Os10g42940

0.000447386

PMID: 24715026, PMID: 10873582

8

LOC_Os01g04050

0.00080268

58

LOC_Os03g03570

0.000446501

PMID: 10364408

9

LOC_Os07g02350

0.000775571

PMID: 16240106, PMID: 11416158

59

LOC_Os12g43550

0.000445728

 

10

LOC_Os08g02640

0.000669873

60

LOC_Os03g49500

0.000444206

PMID: 29767552

11

LOC_Os04g37619

0.000640376

PMID: 24634194

61

LOC_Os10g04674

0.000442469

PMID: 24145853, PMID: 17986178

12

LOC_Os11g35500

0.00062345

PMID:29813124,PMID:29402905

62

LOC_Os10g06740

0.000442469

PMID: 28154240

13

LOC_Os05g41970

0.000594578

PMID: 1731968

63

LOC_Os01g05980

0.000442411

 

14

LOC_Os12g16890

0.000594578

64

LOC_Os10g33650

0.000440094

 

15

LOC_Os01g03680

0.000584668

65

LOC_Os01g18150

0.000438562

 

16

LOC_Os07g10580

0.000564849

PMID: 28158863, PMID: 22108719

66

LOC_Os01g22490

0.000436139

 

17

LOC_Os06g50340

0.000561268

PMID: 19704753, PMID: 16511358

67

LOC_Os02g18550

0.000436139

 

18

LOC_Os10g14150

0.000555163

PMID: 19201764

68

LOC_Os01g46070

0.000435882

PMID: 27820840, PMID: 24793751

19

LOC_Os01g55540

0.000551598

PMID: 15753104

69

LOC_Osm1g00310

0.000432995

 

20

LOC_Os10g22860

0.00054974

PMID: 23384860, PMID: 28101092

70

LOC_Os11g10310

0.000430641

PMID: 28154240

21

LOC_Os10g32990

0.000547737

PMID: 23384860, PMID: 28101092

71

LOC_Os01g24690

0.000428718

 

22

LOC_Osm1g00450

0.000540982

72

LOC_Os01g05870

0.000428516

 

23

LOC_Os01g60670

0.000536737

73

LOC_Os01g05940

0.000428516

 

24

LOC_Os07g11410

0.00053512

74

LOC_Os10g22890

0.000428516

PMID: 28154240

25

LOC_Os01g13800

0.000533159

75

LOC_Os11g04720

0.000428436

 

26

LOC_Os02g13780

0.000533159

76

LOC_Os12g43630

0.000425925

 

27

LOC_Os10g06760

0.000533159

PMID: 23384860, PMID: 28101092

77

LOC_Os10g34990

0.00042449

 

28

LOC_Os10g13970

0.000533159

PMID: 23384860, PMID: 28101092

78

LOC_Os04g36070

0.000423139

PMID: 22806103

29

LOC_Os10g19160

0.000533159

PMID: 23384860, PMID: 28101092

79

LOC_Os09g12290

0.000423054

 

30

LOC_Os02g57530

0.000532385

PMID: 14754915

80

LOC_Os01g18800

0.000420138

PMID: 17535819

31

LOC_Os10g21810

0.000529529

81

LOC_Os06g35540

0.00041931

PMID: 27436282, PMID: 26646386

32

LOC_Os01g47730

0.000507068

82

LOC_Os07g35940

0.000418999

 

33

LOC_Os07g11920

0.000505391

PMID: 28158863, PMID: 22108719

83

LOC_Os01g01060

0.000418677

 

34

LOC_Os01g07870

0.00049357

84

LOC_Os02g12800

0.000418636

PMID: 9742959, PMID: 8148371

35

LOC_Os03g54790

0.000492652

85

LOC_Os07g46750

0.000418636

PMID: 27450495, PMID: 18210155

36

LOC_Os01g18670

0.000492651

86

LOC_Os08g14450

0.000416836

PMID: 21221925

37

LOC_Os07g42300

0.000483507

PMID: 24466124

87

LOC_Os02g53500

0.000412722

PMID: 14756303, PMID: 26781807

38

LOC_Os11g10100

0.000478643

88

LOC_Os12g19381

0.000412026

 

39

LOC_Os11g40150

0.000478361

PMID:28071676

89

LOC_Osp1g00780

0.000410609

PMID:29184886,PMID:27411514

40

LOC_Os12g31370

0.000478361

PMID:28071676

90

LOC_Osp1g01090

0.000410609

PMID:25658309

41

LOC_Os03g05740

0.000472443

91

LOC_Os05g50930

0.000408491

 

42

LOC_Os08g38720

0.000468006

92

LOC_Os10g39440

0.000408336

PMID: 24372780, PMID: 18335199

43

LOC_Os03g50330

0.000462237

93

LOC_Os08g06630

0.000407594

 

44

LOC_Os04g08740

0.000461766

PMID: 19417056

94

LOC_Osp1g00820

0.000407028

PMID:25658309,

45

LOC_Os01g42650

0.000461755

PMID: 16263700

95

LOC_Osp1g01050

0.000407028

PMID:25658309

46

LOC_Os03g27290

0.000460621

PMID: 19217306, PMID: 15672456

96

LOC_Osp1g00420

0.00040642

PMID:25658309

47

LOC_Os10g39670

0.000460227

97

LOC_Os05g49320

0.000404017

 

48

LOC_Os01g65230

0.000459159

98

LOC_Os12g07720

0.000400566

PMID: 14756303

49

LOC_Os03g54780

0.000456546

99

LOC_Os10g06930

0.000399998

PMID: 29356995

50

LOC_Os08g03640

0.000456163

100

LOC_Os03g06410

0.000399411

PMID: 1731968

 

 

Contact

 

Chunyu Wang

chunyu@hit.edu.cn

School of Computer Science and Technology, Harbin Institute of Technolog

Xiangxiang Zeng

xzeng@xmu.edu.cn

School of Information Science and Engineering, Xiamen University

 

 

Copyright © 2018, Xiamen University and Harbin Institute of Technolog Units