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