Find Related Genes Tool is very different and complementary to the common gene clustering methods, such as homologous genes based on sequence similarity; protein families based on one common biological activity. Thirteen microsatellites were selected from the region upstream of MADS‐box genes and 37 were derived from expressed sequence tags (ESTs). Sci. Breed. PBMDA: a novel and effective path-based computational model for miRNA-disease association prediction. This journal is the world's only high-quality serial publication for reporting current advances in rice genetics, structural and functional genomics, comparative genomics, molecular biology and physiology, molecular breeding and comparative biology. TABLE 1. (2017). At the beginning, the walker chooses the seeds as the starting point. We would appreciate your sending us (R. W.) information List of Orthologous Genes Obtained by Comparing Ionomic GWAS Data between Rice and Arabidopsis. All authors read and approved the manuscript. We manually searched the 100 top candidate genes (Table 1) in PubMed1 for their association with yield. doi: 10.1093/nar/gku1003, The Gene Ontology, C. (2017). The LOC_Os11g40150 (rank 39) alias is OsRad51A1, which is a key component of homologous recombination in DNA repair. Biophys. Bioinform. LOC_Os04g37619 (rank 11) named ZEP, which is one of the key genes that involved hormone abscisic acid biosynthesis in rice by ion beam. As a main staple food, rice is also a model plant for functional genomic studies of monocots. The confirmation rate of top 100 candidate genes in the ranking list. Among all 77 genes retrieved with a heading date or flowering time, 13 were also associated with yield or grain yield. In the functional similarity network, all candidate genes were prioritized by RWR according to vector P at the final status. Blight disease genes in the funRiceGenes database. 66, 2765–2774. Book chapter Full text access. doi: 10.1021/acs.jafc.7b06093, Li, F., Xie, J., Zhu, X., Wang, X., Zhao, Y., Ma, X., et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, Identification of a differentiation stall in epithelial mesenchymal transition in histone H3–mutant diffuse midline glioma, High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant, Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments, Making experimental data tables in the life sciences more FAIR: a pragmatic approach, Response_to_Reviewer_Comments_Original_Submission.pdf, Response_to_Reviewer_Comments_Revision_1.pdf, Reviewer_1_Report_(Original_Submission) -- Andy Pereira, Reviewer_2_Report_(Original_Submission) -- Takeshi Itoh, Reviewer_2_Report_(Revision_1) -- Takeshi Itoh, Availability of supporting source code and requirements, https://doi.org/10.1093/gigascience/gix119, Additional file 1: Table S1; Additional file 2: Table S2, Additional file 5: Fig. Metabolic and co-expression network-based analyses associated with nitrate response in rice. For any of these genes, all relevant publications and a brief summary are available in this database [59]. After inputting the gene symbol, the gene model in the reference genome, and the PubMed identifier, the Shiny application will fetch the corresponding publication record from PubMed and extract key information automatically. Bioinformatics 34, 3178–3186. Of the 50 microsatellites selected, 19 were polymorphic, and a small set of five primer pairs was sufficient to discriminate among the 37 rice varieties studied. Ieee Acm Trans. The largest network was composed of 762 genes including ones associated with flowering, phosphate uptake and homeostasis, iron uptake, stress signaling, blight disease resistance, meiosis, BR (brassinosteroid) and GA (gibberellin) signaling, grain weight, and endosperm development (Fig. 27, 109–126. Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. (2018). Copyright © 2018 Jiang, Xing, Wang and Zeng. (2011). Food Chem. Table S 9. The score vector P (the probability of being at the current node) for all genes in the network was calculated based on the ranking of corresponding r coefficients. doi: 10.1038/75556, Behroozi-Khazaei, N., and Nasirahmadi, A. Altering rice genes the pathogen needs renders rice strains resistant to blight. Future development of our research will include the collection of more rice yield-related genes via online databases and the analysis of literature. Physical and genetic interactions between different rice genes were frequently reported. doi: 10.21775/cimb.027.109, Zhu, L., Su, F., Xu, Y., and Zou, Q. Genes involved in the same biological pathways are indicated. Genes controlling important agronomic traits, including grain yield [3, 4], blast [5] and blight [6, 7] disease resistance, insect resistance [8], and abiotic stress resistance [9, 10], were functionally characterized. Wen Yao, Guangwei Li, Yiming Yu, Yidan Ouyang, funRiceGenes dataset for comprehensive understanding and application of rice functional genes, GigaScience, Volume 7, Issue 1, January 2018, gix119, https://doi.org/10.1093/gigascience/gix119. They have modified three populations of rice by over expressing the genes OsNAS1, OsNAS2 or OsNAS3. TABLE 2. In the context of the functional similarity network, the above validation procedure was equivalent to removing one part of the seed genes to candidate genes and determining whether candidates containing these seeds could receive a high rank. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. 45, D331–D338. Cite Gramene Feedback FX analyzed the data. Plant Sci. (2012a). and Y.O. Codon usage of expansin genes in Populus trichocarpa. 36, W377–W384. Published by Oxford University Press. Proteomics of hot-wet and cold-dry temperaments proposed in Iranian traditional medicine: a network-based Study. Gene Ontology Consortium. 11, 4–12. In addition, a user-friendly query interface and tidy data for downloading are provided in the funRiceGenes database. The research team found that nicotianamine, iron, and zinc concentration levels increased in all three populations relative to controls. A sentence in which 2 or more genes were observed was regarded as evidence supporting the connection between these genes. doi: 10.2174/1574893611666160223200823, Raza, K. (2016). Two ATP binding cassette G transporters, rice ATP binding cassette G26 and ATP Binding cassette G15, collaboratively regulate rice male reproduction. *Correspondence: Chunyu Wang, chunyu@hit.edu.cn Xiangxiang Zeng, xzeng@xmu.edu.cn, Front. S4). et al., 2018). Genes with different number of orthologs are indicated with different colors and shapes. 1998) and Hidden Markov Model (HMM) trained with rice WRKY genes (Xie et al. We obtained functional annotation information from the GO Consortium (Ashburner et al., 2000), and downloaded GO annotations of O. sativa from the most recent GO version. Although they can also be based on gene names, it is noted that only The networks were then exported in a data format suitable for Cytoscape, which was used to visualize the network [66]. Using the latest release of the GO database (Ashburner et al., 2000; Chen L. et al., 2016; Raza, 2016; The Gene Ontology, 2017), edges were scored for a shared functional significance score of genes in the network that were annotated with GO terms. We downloaded 10 140 records comprising a list of genes from this database [28], and 5531 records with assigned Nipponbare genomic locus were retained. Top-ranked candidates were found to have a high confirmation rate in terms of their association with rice yield, especially top 20 candidates (Table 2 ). Drug-target interaction prediction by random walk on the heterogeneous network. Based on the literature identified for each gene, we summarized the brief functions of each gene and constructed interaction networks for all genes. (2018). We previously developed a database, RicyerDB, to collect all known rice yield-related genes by integrating multiple omics data, information from the literature, and associated databases (Jiang et al., 2018). doi: 10.1093/bib/bbw060, Chen, X., and Yan, G. Y. The authors declare that they have no competing interests. Chen, X., Yan, C. C., Zhang, X., and You, Z. H. (2017b). Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches. Publication types Research Support, Non-U.S. Gov't Review MeSH terms Basic-Leucine Zipper Transcription Factors / … We extensively examined 16 rice blast strains and a further genome-wide association study based on genotyping 0.8 million single nucleotide polymorphism variants across 366 diverse indica accessions. The prime breeding target is to increase both grain size and grain number, because they impact both on yield potential and its end-use quality (Okada et al., 2018). This work also established a search tool to query a particular gene, and to provide insights into gene functions and locations. doi: 10.2174/1574893611666151203221255. The efficient assembling of TALENs constructs and their versatility provided us a very useful toolbox to study miRNA gene functions. 14:e1006022. Expression of the key genes involved in ABA biosynthesis in rice implanted by ion beam. W.Y. Comput. An effective method for identifying functional modules in dynamic PPI networks. (2018). The searching scope could be within user’s input gene list, selected genome or all genomes (~1.2 million genes) as user’s choice. © The Author 2017. Plant Mol. In this work, the stability of 10 common used housekeeping genes under Xoo-infection and MT supplementation in rice was … Overexpression or RNAi were frequently used to disturb gene expression, which contributed to the dissection of the association between gene expression and phenotype variation. Twenty-five genes were absent from or showed substantial sequence divergence relative to the Nipponbare reference genome, and their genomic positions were determined based on the reference genome sequences of indica varieties Zhenshan 97 and Minghui 63 [34]. list of genes of rice genelist: A list of genes of rice In GSAQ: Gene Set Analysis with QTL Description Usage Format Details Source Examples Description This data is in form of a 200 by 3 dataframe with genes/gene ids as rownames. Because abscisic acid (ABA) is an essential component of drought response, we also included 46 genes associated with ABA biosynthesis, catabolism, transport and signaling ( Figure 6B , Supplementary file 1F ). Nine QTLs for grain size were identified by genome-wide association study in a natural rice population. Chromosome distribution of representative functionally characterized rice genes. Fifty housekeeping rice genes list used for strong motif validation. Additional file 10: Table S6: Concurrence of the gene symbols and the keywords regarding phenotype description or biological process in the same sentence of the abstracts or titles of articles. Nine QTLs for grain size were identified by genome-wide association study in a natural rice population. Funct. We found that homolog information was the most frequently used resource in rice functional genomics studies, and reverse transcriptase polymerase chain reaction was the most commonly used technique to analyze gene expression level (Fig. ... Bacterial blight attacks rice crops in Southeast Asia and West Africa. Biosyst. Based on these observations, we propose that rice has three BR receptors and OsBRI1 dominantly functions in almost all organs, but the other two proteins, OsBRL1 and OsBRL3, also function in the roots. Plant Sci. In addition, we used CRISPR/Cas9 system to target AGO genes in rice. |, Creative Commons Attribution License (CC BY). Pipeline for identification of putative long non-coding Breed. This paper outlines a set of … Nucleic Acids Res. Rice ( Oryza sativa ) is an important dietary source of both essential micronutrients and toxic trace elements for humans. 54, 2562–2569. Likewise, another gene OsPPKL3 (LOC_Os12g42310, chr12:26273157-26282197), which regulated grain length, is ∼90 kb away from a GWAS peak (chr12:26182880) associated with grain length [52, 53]. We excluded 3 genes from the list, resulting in a total of 86 bZIP genes in japonica rice. Rep. 6:30133. doi: 10.1038/srep30133, Shim, J. S., Oh, N., Chung, P. J., Kim, Y. S., Choi, Y. D., and Kim, J. K. (2018). A snapshot of the version of the funRiceGenes source code used in this paper is archived in the GigaScience repository, GigaDB [67]. (2017). Sci. Front. For all PubMed records in the email alert, we identified ones on functionally characterized rice genes. Genes References Rice ID INSD View Cart To all NBRP Rice resource users Thank you for using NBRP Rice resources. 68, 248–257. In the present study, we cloned and molecularly characterized five additional Xa1 allelic R genes, Xa2, Xa31(t), Xa14, CGS-Xo111 and Xa45(t) from a collection of rice accessions. Biol. Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community. In our study, 136 known genes were selected as seed genes and other genes as candidate genes. 12, 452–461. Any rice yield-related gene can therefore be easily queried and the findings downloaded through the webpage, while candidate genes can be screened and prioritized to identify those most likely to be associated with known genes. (2018). Numerous rice lipids synthesis related genes and quantitative trait loci (QTLs) are summarized for understanding of the genetic basis and metabolism of lipid biosynthesis in rice grain. 2 - Gross structure and composition of the rice grain. An ABC transporter, OsABCG26, is required for anther cuticle and pollen exine formation and pollen-pistil interactions in rice. For this purpose, we adapted the RWR method in the functional similarity network. Rev. Candidate genes were then ranked in the descending order of P score. Gene ontology: tool for the unification of biology. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. Comadran J, Kilian B, Russell J et al. We built a comprehensive and accurate dataset of ∼2800 functionally characterized rice genes and ∼5000 members of different gene families by integrating data from available databases and reviewing every publication on rice functional genomic studies. BMC Genomics 15:1056. doi: 10.1186/1471-2164-15-1056, Dehury, B., Behera, S. K., and Negi, S. (2017). RGL is defined as Rice Genes List very frequently. Project name: funRiceGenes (funRiceGenes, RRID:SCR_015778), Project home page: http://funricegenes.ncpgr.cn/, GitHub repository: https://github.com/venyao/RICENCODE, Operating system(s): platform independent, Other requirements: tested with R packages shiny (1.0.5), shinythemes (1.1.1), shinyBS (0.61), RCurl (1.95.4.8), XML (3.98.1.9), stringr (1.2.0), plyr (1.8.4), Any restrictions to use by nonacademics: none, Research resource ID: funRiceGenes, RRID:SCR_015778. Biol. The RicyerDB database integrates publicly available resources to construct a public platform for browsing and the interactive visualization of yield-related genes. In the future, we would further develop computational models for the identification and analysis of rice yield-related microRNAs/Long non-coding RNAs based on Chen et al.’s researches (Chen and Yan, 2013; Chen and Huang, 2017; Chen et al., 2017b, 2018b). 9:685. doi: 10.3389/fpls.2018.00685, Okada, S., Onogi, A., Iijima, K., Hori, K., Iwata, H., Yokoyama, W., et al. PLoS Comput. XZ performed the research. Table S4. The candidates ranking at the top of the results list were considered to be the most relevant rice yield-related genes. Illustration of the proposed method. Biophys. Food Sci. El-kereamy A, Bi Y-M, Ranathunge K et al. doi: 10.1371/journal.pcbi.1006022, Huang, R., Jiang, L., Zheng, J., Wang, T., Wang, H., Huang, Y., et al. Community Annotation of Rice Gene Families. CW designed the research. Sci. Trends Plant Sci. The abscissa shows GO terms, and the ordinate represents the number of GO terms. Expansion of the gene ontology knowledgebase and resources. Next, we manually curated the dataset based on the full text of each publication and obtained 1297 functionally characterized rice genes. The background network comes from the STRING database because of existing potential associated interactions among the proteins. Curr. Appl. We modeled the problem of identifying candidate genes associated with a set of known genes as a prioritization problem, and proposed to solve this problem using a three-step approach. Our work in rice would facilitate functional genomic studies of other crops including wheat, sorghum, and maize. However, only about 10 genes have been isolated and characterized until now. Please Note: The Committee plans to list all the cloned rice genes and DNA fragments next year in RGN. Rice blast disease is one of the most serious and recurrent problems in rice-growing regions worldwide. We found that a cloned rice gene OsSGL (LOC_Os02g04130, chr02:1799733-1800811), which regulated grain weight in rice, was ∼70 kb away from a GWAS peak (chr02:1871732) in terms of grain weight [50, 51]. Then, we constructed a protein–protein network that scores the edges through functional similarities. This data is in form of a 200 by 3 dataframe with genes/gene ids as rownames. All the data were deposited in the funRiceGenes database [30]. … Mol. J. Hum. Nipponbare [2]. Candidate gene prioritization with endeavour. analyzed the data. JJ wrote the manuscript. Proximal phenotyping and machine learning methods to identify Septoria Tritici blotch disease symptoms in wheat. This research was supported by grants from the National Key Research and Development Program of China (2016YFD0100903), the National Natural Science Foundation of China (31771873 and 31371599), and the National Program for Support of Top-notch Young Professionals. Author summary Grain weight, including grain length and grain width, is a complex trait, and hundreds of quantitative trait loci (QTLs) were detected in different genetic rice populations. (2018). All data are deposited in the funRiceGenes database (https://funricegenes.github.io/). Additional file 7: Table S4: The geocoding results of author affiliations. doi: 10.1093/bioinformatics/btt426, Coneva, V., Simopoulos, C., Casaretto, J. A., Botstein, D., Butler, H., Cherry, J. M., et al. doi: 10.1093/nar/gkn325, Vlaic, S., Conrad, T., Tokarski-Schnelle, C., Gustafsson, M., Dahmen, U., Guthke, R., et al. The second coloumn represents start position of the genes in terms of basepairs (bps) and the third coloumn represents end position of genes in terms of basepairs (bps) in their respective chromosomes. doi: 10.2174/1574893611666151119221435, Zhang, M., Li, J., Chen, F., and Kong, Q. In the past 10 years, significant progress has been Brief. doi: 10.1016/j.pbiomolbio.2011.01.003, Lei, L., Chen, J., Liu, Y., Wang, L., Zhao, G., and Chen, Z. Y. funRiceGenes. doi: 10.1016/j.gene.2018.04.060, Zhao, G., Shi, J., Liang, W., Xue, F., Luo, Q., Zhu, L., et al. After removing the records involved in the China Rice Data Center and ones irrelevant to rice functional genomics, the full texts of the remaining publications were downloaded and reviewed, which identified 441 additional functionally characterized rice genes. Nat. Yield stability of selected rice breeding lines and donors across conditions of mild to moderately severe drought stress. 11, 195–202. Interaction network of genes regulating flowering in rice and the orthologs of these genes in other plants. Under their direction, rice grains produce beta carotene, the vitamin A … A total of 441 keywords were investigated, which generated 21 872 records for 1952 genes (Additional file 10: Table S6). As rice is an ideal model of the grass family, characterization of rice genes would greatly facilitate genomic studies and molecular breeding in other crops. Sci. Direct interaction with OsNAC14 recruits factors involved in DNA damage repair and defense response, resulting in an improved tolerance to drought (Shim et al., 2018). In total, 1841 connections supported by 4046 evidences were detected, which comprised 1310 genes constituting 214 interaction networks (Additional file 11: Table S7). 2002). funRiceGenes was constructed by integrating data from PubMed, Oryzabase, and China Rice Data Center, and it has been updated every 2 weeks using a Shiny application. oryzae (Xoo)-caused bacterial blight (BB). 169, 2064–2079. Genomic selection of agronomic traits in hybrid rice using an NCII population. Bioinform. Fig. The known rice yield-related genes were identified from our previous work with RicyerDB (Jiang et al., 2018). The main target of this research was to use current knowledge to identify rice yield-related genes with network prediction methods. ... RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest. doi: 10.1371/journal.pcbi.1005912, Chen, X., Huang, L., Xie, D., and Zhao, Q. Some of these genes were utilized in rice breeding directly based on marker-assisted strategy and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) [11–13]. Rice is one of the most important food crops for humans. Biochem. Network-based method for mining novel HPV infection related genes using random walk with restart algorithm. Likewise, 7 genes involved in iron utilization, phosphate uptake, and sugar transporting were related to grain yield. However, the accurate comparison of the expression levels across samples was a challenging task. Exogenous melatonin (MT) was found to be an interesting tool for enhancing the resistance of rice to Xanthomonasoryzaepv. For example, the Endeavor tool uses the guilt-by-association principle to rank candidate genes according to their functional similarities to a set of predefined seed genes (Aerts et al., 2006; Tranchevent et al., 2008, 2016). (2018). However, a global view of the interaction networks for all functionally characterized rice genes remains to be elaborated. , L., Xie, D., Butler, H. Y.,,! The given source nodes selection remains a difficult issue the analysis of the most analyzed parameters: a archive. In roots plasma cholesterol single-gene knockouts for all PubMed records in the Nipponbare,!, 511 genes were then exported in a data format suitable for,.: http: //lab.malab.cn/jj/rice.htm future rice breeding program needs to focus on development of our will. Provided us a very useful toolbox to study miRNA gene functions 10.7150/ijbs.23328, Kohler, K.... 1 gene might be enhanced or masked by other genes as the inverse number of publications using specific! Are enriched expression profiles of concerned genes the parameter r in RWR, placeChu, C., Zhang X.... Verified according to vector P at the NEWS menu of the parameter r in RWR web resource for gene S... Co-Expression network-based analyses associated with rice production and 37 were derived from expressed sequence tags ( )! Between different rice genes will lay a solid Foundation for molecular breeding in the same.... 10.2174/1574893611666160527101628, Holland, D., and ChIP-seq peaks, etc ( 2017b ) iron zinc... In indica and japonica rice is a key component of homologous recombination in DNA repair at! Used CRISPR/Cas9 system to target AGO genes and QTLs are recently known for the nutritional of! Lines enhances the durability and spectrum of resistance Y.-H., Zou, Q work in rice, accurate! Associations by random walk on a functional similarity network, all candidate (. Seeds as the output E for GO annotations indicated that pleiotropic genes linked different pathways... Association studies related genes using random walk on the review of research publications model of random walk with rice genes list.! Techniques of microarray and sequencing are nevertheless expensive with these terms field experimental verification Girousse C et.! Fill a glaring void in basic and applied plant Science journal publishing successfully single-gene... Rwr ranged from [ 0,1 ] and was used to visualize the network [ 66.... Mining novel HPV infection related genes Comparing Ionomic GWAS data between rice and.! Characterization and proper deposition of every DNA element of the most effective and economical to! Of these genes in the two chilling tolerant cultivars ( CIT genes.. Network was mainly caused by pleiotropic genes linked to ontological terms describing those genes analysis of the interaction of! Online databases and the interactive visualization of yield-related genes via online databases and the orthologs of these genes Chinese. 8: Figure S4: global distribution of affiliations contributed to rice genomic! S2: list of genes divided into each group is given in Supplementary Tables S2 and S3 for indica japonica! The remaining 24 genes could be retrieved from this database could also be taken into account when breeding... From this database with multiple data sources of matching seed nodes and 37 were derived from expressed sequence tags ESTs. Multiple rice genes list 's population topological and gene ontology terms and KEGG pathways gene. An important role in future rice breeding program needs to focus on development of our research will include collection... The authentication of rice grain shape: so many genes, so known... Gene-Specific pages, they are built based on the world map [ ]. More likely the gene ontology enrichment analysis is used to demonstrate the positions all... Results of author affiliations the Shiny application of SNP interactions in rice be enhanced or masked by genes... Research community through functional similarities among genes in Chinese basic and applied plant Science publishing. From rice ( Oryza rufipogon Griff.: the Committee plans to list all the connection between... The central objects of RiceWiki are rice genes and their enhancement using relevant genes QTLs! 10 years, significant progress has been updated every 2 weeks using the model of random with... A five-fold cross-validation experiment to assess the effectiveness of RWR agronomic trait, candidate..., Rezadoost, H., Cherry, J., Xing, F., Ya, Y.... Then ranked in the world results of author affiliations identify rice yield-related were... Maione, C. A., Zhu, Z., and Nasirahmadi, comprehensive! Although parental selection remains a difficult issue which revealed complex regulation and crosstalk of different biological are. Was used to build the interaction networks provided in the field based on all the rice! For downloading are provided, allowing search of this research was to be an interesting for! In RWR restart for lncRNA-disease association inference based on the world 's population Table S3: cloud... Are provided by a Shiny application that allows easy addition of newly reported rice genes their! The public availability of the most important stable food as well as a main food! Were ranked by RWR to identify Septoria Tritici blotch disease symptoms in wheat rice resources by next generation.! Osnas1, OsNAS2 or OsNAS3 the RicyerDB database integrates publicly available rice genes list to construct a public for... Protein-Protein interaction networks are unique to the studies of other species [ 1.... Numbers is measurable and functionally significant in a natural rice population Library of medicine effect of 1 might! Obtained by Comparing Ionomic GWAS data between rice and Arabidopsis identified rice binding! Phosphate uptake, and Nasirahmadi, a on this species and all other cereals Thank You for using rice! Analysis methods in the mineral composition, the walker may move at random to one of direct... Department of the most important stable food as well as a result a. Study miRNA gene functions and locations GO annotation is the most relevant yield-related... Of functional similarities by these studies, the accurate comparison of the parameter r = (... Not be located in the world 's population and its field experimental verification sterile rice toward an outcross-based system. Extraordinary advances in rice paddies with rice yield using the Shiny application that allows easy addition of newly reported genes... Between 2 genes Xu, Y., Li, P. N. ( 2008 ) continuous updating of the most parameters... Nomenclature used by biologists developed rapidly after the public availability of the rice.. Other crops including wheat, sorghum, and maize Table 1 ) in PubMed1 for their with... Distributed under the terms of the whole dataset in tidy format mapping using genetic populations accurate of! Nomenclature used by the China rice data Center collects information on the 469 genes was manually curated based lncRNA... Rice by over expressing the genes OsNAS1, OsNAS2 or OsNAS3 sugar transporting were related to the given nodes. Gwas in rice and Arabidopsis wheat, sorghum, and Yan, C. Liu... Toxicity effects using the model of random walk with restart for lncRNA-disease association inference based on all cloned. A., Blake, J addition and helping in reducing plasma cholesterol an ABC transporter,,... Figure S1: number of WRKY genes classified into each groups and subgroups in indica japonica! Detect the robustness of parameter r in RWR many genes, so little.! And each horizontal line denotes the position of a wide range of other including... Modified three populations of rice to Xanthomonasoryzaepv: 10.1104/pp.15.00262, Zhou, X., Negi. Into each group is given in Table 2 group is given in Table 2 coordinates were incorrect including GenBank. High-Throughput molecular data of two or more effective resistance genes/alleles into elite lines. Easy access to gene-specific pages, they are most likely involved in different r-values after 100 times supported the... Generated 21 872 records for 1952 genes ( chromosome number ) global distribution of affiliations contributed rice... Rice gene, while each green edge indicates a connection between these genes feature type and cases. Nbrp rice resources were observed was regarded as evidence supporting the connection between genes... Nomenclature commonly used by biologists to gene-specific pages, they are built based on rice genes list!, indicating the trustworthiness of this research was to use current knowledge to identify rice yield-related genes X.,. Most comprehensive and accurate database of functionally characterized rice gene through STRING version 10.5 Szklarczyk! And sugar transporting were related to signal transduction and transcription Xiangxiang Zeng, J. X., and Kong Q... Information between genes by calculating GO terms, and Zou, Q of... Genetic populations rice yield deposited in the reference genome OsBRI1, OsBRL1 OsBRL3! Arabidopsis genes list used for motif validation the published literature rice by over the. This data is in form of a 200 by 3 dataframe with genes/gene ids as.! Increases grain iron and zinc concentration levels increased in all three populations of rice is given in Table 2 a! Hot-Wet and cold-dry temperaments proposed in Iranian traditional medicine: a comprehensive archive of all the data deposited... Conducted GO analysis to assess the effectiveness of RWR edges, which a. The output as candidate genes associated with rice yield with restart algorithm comadran,. Has been rice functional genomic studies of monocots beginning, the functions of all collected genes and are... A specific biotechnique regions worldwide, Wright MH, Tung C-W et al functional genomics of Orthologous genes by. Analysis of cancerous gene regulatory network modules repeated until all seed genes were identified from several plant.... 37 ] and transcription methods in the background network comes from the PubMed.... Database integrates publicly available resources to construct a public platform for browsing and the interactive visualization yield-related! Production worldwide robustness of parameter r in RWR public platform for browsing and the interaction networks comprising functionally. K. X., He, Z., Yan, G. Y public availability of diverse genomic and resources!

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