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 School of Computer
Science and Technology, Harbin Institute of Technolog |
Xiangxiang
Zeng School of
Information Science and Engineering, Xiamen University |
Copyright © 2018,
Xiamen University and Harbin Institute of Technolog Units |