Abe, K., Oshima, M., Akasaka, M., Konagaya, K. I., Nanasato, Y., Okuzaki, A., et al. We also kept track of new records in the database of Oryzabase and China Rice Data Center, which were then added to our database using the Shiny application. In our application, the initial probability vector P0 was constructed such that equal probabilities were assigned to the nodes representing members of the disease, with the sum of the probabilities equal to 1. In each step of the walking process, the walker may start on a new journey with probability r or move on with probability 1−r. to investigate lost/acquired genes during rice domestication Fantao Zhang1†, Tao Xu2†, Linyong Mao3, Shuangyong Yan4, Xiwen Chen5, Zhenfeng Wu6, Rui Chen7, Xiangdong Luo1, Jiankun Xie1* and Shan Gao5* Abstract Background: It is widely accepted that cultivated rice (Oryza sativa L.) … 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]. To achieve this goal, several approaches have been proposed from the perspective of computational systems biology (Behroozi-Khazaei and Nasirahmadi, 2017; He et al., 2017; Liu E. et al., 2017; Liu Y. et al., 2017; Xiong et al., 2017; Maione and Barbosa, 2018; Zhang M. et al., 2018; Zhou et al., 2018). 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. TABLE 1. Dietary wheat bran oil is equally as effective as rice bran oil in reducing plasma cholesterol. The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. S3). Decoding the genetic reservoirs of rice is the basis for rice phenotype improvement. Blight disease genes in the funRiceGenes database. Bioinformatics 29, 2617–2624. All records were grouped by published journal. 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). Table S 9. Xu et al. In accessing pseudomolecule data from the Rice Genome Annotation Project web site, terms used internally by the Rice Genome Annotation Project such as TU and gene model can be found. Gene prioritization through genomic data fusion. Pipeline for identification of putative long non-coding Walking the interactome for prioritization of candidate disease genes. A Shiny application [31] was then developed to facilitate utilization of this dataset, which also enabled easy addition of newly reported genes to the database. doi: 10.1016/j.fcr.2016.09.011, Tranchevent, L. C., Ardeshirdavani, A., ElShal, S., Alcaide, D., Aerts, J., Auboeuf, D., et al. Acta Mol. New genes were added to this database using the Shiny application, based on daily email alerts of search results from the PubMed database with the keyword rice (rice[Title] OR rice[Title/Abstract]) [32]. View 0 peer reviews of Rice histone deacetylase genes display specific expression patterns and developmental functions on Publons COVID-19 : add an open review or score for a COVID-19 paper now to ensure the latest research gets the extra scrutiny it needs. Nutr. Plant Sci. All candidate genes were ranked by RWR to determine the ranking of the test gene. 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. Additional file 2: Table S2: List of rice gene families. When two genes, i and j, have m functions in common, i.e., F(i)∩F(j) = (f1, f2, …, fm), F(i,j) was given as the total sum of the significance of the functions shared between them as follows: Here sig(fn) denotes the significance of a function fn(n = 1,2,..., m) shared between genes i and j, | Genes (fn)| is the number of genes sharing a function fn. In addition, a user-friendly query interface and tidy data for downloading are provided in the funRiceGenes database. Gramates LS, Marygold SJ, Santos Gd et al. In this work, the stability of 10 common used housekeeping genes under Xoo-infection and MT supplementation in rice was … We further downloaded 29 982 publication records by querying the PubMed database with the keyword rice ((rice[Title] OR rice[Title/Abstract]), data until 13 February 2014). Bioinform. Rice 11:32. doi: 10.1186/s12284-018-0223-4, You, Z. H., Huang, Z. Finally, the top candidate gene was verified according to its function and by the published literature. Two added genes turn rice golden, one from maize and one from a soil bacterium. As an integrated rice science database, Oryzabase [25] also provides information on a portion of functionally characterized rice genes with manual curation. Brief. doi: 10.1371/journal.pcbi.1006022, Huang, R., Jiang, L., Zheng, J., Wang, T., Wang, H., Huang, Y., et al. Second, the interaction network provides a systematic view of functional similarities between genes by calculating GO terms. Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis. We manually searched the 100 top candidate genes (Table 1) in PubMed1 for their association with yield. Taken together, of the top 100 candidate genes in the ranking list, 46 candidate genes predicted by our method had been confirmed to be correlated with rice yield in PubMed literature (Table 1). https://funricegenes.github.io/ https://funricegenes.github.io/ At the homepage of our database, we provide the download of the whole dataset in tidy format. Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Plant Sci. doi: 10.2174/1574893611666160115212806, Rezadoost, H., Karimi, M., and Jafari, M. (2016). 18:89. doi: 10.1186/s12863-017-0559-6, Liu, Y., Zeng, X., He, Z., and Zou, Q. The searching scope could be within user’s input gene list, selected genome or all genomes (~1.2 million genes) as user’s choice. As far as we are concerned, this is the most comprehensive and accurate database of functionally characterized rice genes with continuous updating. 2002). et al., 2018). doi: 10.2174/1574893611666160223200823, Raza, K. (2016). A sentence in which 2 or more genes were observed was regarded as evidence supporting the connection between these genes. (2018). Based on massive expression profiles, RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest. First, the RWR method can predict associations among known seed genes and candidate genes with the ability to spread the information that known seeds carried via their neighbors. 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. 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. 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). C. Price, 1989. Analyses of these data usually identify differentially expressed genes, gene co-expression networks, differentially methylated regions, and ChIP-seq peaks, etc. 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). Genes related to signal transduction and transcription category may play an important role in transduction and regulation of upstream signals mediated by Al in rice bean because they represent one of the major categories in both forward libraries. Mol. doi: 10.2174/1574893611666151119221435, Zhang, M., Li, J., Chen, F., and Kong, Q. genes in rice breeding, were defeated in fields due to the rapidly emerging virulent strains 84 of Xoo pathogen (Vera Cruz et al., 2000; Adhikari et al., 1999; Lee et al., 1999). Biol. doi: 10.1007/s13197-017-2701-x, Borzee, A., Heo, K., and Jang, Y. Once rice is attacked by M. oryzae, pattern recognition receptors (PRRs) on the cell surface can specifically recognize pathogen-associated molecule patterns (PAMPs), and activate defense response by cell wall modification, callose deposition, and via … Fifty housekeeping rice genes list used for strong motif validation. Wu, T. Y., Gruissem, W., and Bhullar, N. K. (2018). 1860, 2619–2626. Community Annotation of Rice Gene Families. doi: 10.21775/cimb.027.109, Zhu, L., Su, F., Xu, Y., and Zou, Q. IRWRLDA: improved random walk with restart for lncRNA-disease association prediction. Published by Oxford University Press. In this study, we constructed a comprehensive, up-to-date database of rice functional genes, which includes ∼2800 cloned rice genes and ∼5000 members of different gene families. Biol. Rep. 8:2792. doi: 10.1038/s41598-018-21163-w, Zhang, X. D., Zhao, K. X., and Yang, Z. M. (2018). Irritation can enhance the expression of genes involved in ABA biosynthesis, resulting in increasing content of endogenous plant hormone abscisic acid in rice (Chen et al., 2014). Based on the literature identified for each gene, we summarized the brief functions of each gene and constructed interaction networks for all genes. Curr. (2000). Overexpression or RNAi were frequently used to disturb gene expression, which contributed to the dissection of the association between gene expression and phenotype variation. (2018). Bioinform. The authors declare that they have no competing interests. PLoS Comput. 4; Additional file 13: Table S8). Bednarek J, Boulaflous A, Girousse C et al. (2016). doi: 10.2174/1574893611666161008195145, Li, M., Zheng, R. Q., Li, Q., Wang, J. X., Wu, F. X., and Zhang, Z. H. (2016). Biosyst. All data are deposited in the funRiceGenes database (https://funricegenes.github.io/). The work was supported by the Natural Science Foundation of China (Nos. For example, Ghd8 was responsible for grain number, plant height, and heading date [37]. Bioinform. Genes and QTLs are recently known for the nutritional quality of rice. Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches. BMC Genomics 15:1056. doi: 10.1186/1471-2164-15-1056, Dehury, B., Behera, S. K., and Negi, S. (2017). and Y.O. Genetic bases of rice grain shape: so many genes, so little known. Acta Gen. Sub. As of 23 February 2017, ∼2800 functionally characterized genes and ∼5000 gene family members were archived in the funRiceGenes database, which accounted for 19.2% of the 39 045 annotated protein-coding rice genes (Additional file 1: Table S1; Additional file 2: Table S2) [33, 23]. STRING v10: protein-protein interaction networks, integrated over the tree of life. Breed. Articles, College of Pharmaceutical Science, Zhejiang University, China. J. Biol. An ABC transporter, OsABCG26, is required for anther cuticle and pollen exine formation and pollen-pistil interactions in rice. All the affiliations are marked on the world map as blue circles based on their longitudes and latitudes. Biosyst. Thus, the gene interaction networks provided in this database could also be taken into account when making breeding designs. Identification of QTLs for rice grain size using a novel set of chromosomal segment substitution lines derived from Yamadanishiki in the genetic background of Koshihikari. Biosyst. View all The shared functional significance score F(i,j) between gene i and j was measured by the Weighted Shared Functions approach, which considered a gene’s functions as a set of functional categories in GO. Comparative analysis with one other chilling tolerant rice and two chilling sensitive rice resulted in identification of 182 genes that were cold induced in all four rice cultivars (CCI genes). Candidate gene prioritization with endeavour. (2016). We calculated the ranking score, p, for each gene in the disease-related network and ranked these genes in the descending order of p. We achieved the goal of identifying candidates related to known seeds by calculating a score for each candidate and then ranking the candidates to obtain a ranking list. The GENE menu lists 2900+ Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community. Biol. List of primers used for qRT-PCR analysis. (2018) used machine learning and integrated this analysis with data obtained from spectroradiometer, infrared thermometer, and chlorophyll fluorescence measurements to identify the most predictive proxy measurements for studying Septoria tritici blotch disease of wheat. McCouch SR, Wright MH, Tung C-W et al. Finally, the parameter r = 0.3 was selected to calculate vector P to obtain the ranking results. An overview of SNP interactions in genome-wide association studies. (2018). Our work in rice would facilitate functional genomic studies of other crops including wheat, sorghum, and maize. 12, 624–633. (2018). Curr. Pipeline for identification of putative long non-coding RNAs in rice. Bioinform. 68, 248–257. The purpose of this page is to explain the nomenclature used by the project and relate it to nomenclature commonly used by biologists. These results demonstrated the increasing degree of conservation of the flowering pathway among plants with closer phylogenetic relationships, implying substantial value of knowledge on functionally characterized rice genes to future dissection of flowering time regulation in other crops. LOC_Os04g37619 (rank 11) named ZEP, which is one of the key genes that involved hormone abscisic acid biosynthesis in rice by ion beam. In this study, we built a comprehensive and accurate database of functionally characterized rice genes, funRiceGenes, which provides a valuable resource for rice functional genomic studies. List of primers used for qRT-PCR analysis. Genet. … S5). 13:e1005912. 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. 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. Rice is the most important food crop worldwide. The functions of OsSGL and OsPPKL3 were characterized by transgenic studies, and the natural variations of the 2 genes are yet to be dissected. This procedure applied a RWR algorithm to the network to calculate a score for each candidate gene, and then ranked the candidates to obtain a ranking list as the output (Chen et al., 2012a,b; Chen, 2016; Chen X. et al., 2016; Li et al., 2016; Peng et al., 2016; Zhu et al., 2018). Analysis of the chemical toxicity effects using the enrichment of Gene Ontology terms and KEGG pathways. Each node represents a functionally characterized rice gene. Curr. In total, ∼3553 publications with respect to ∼2800 functionally characterized genes were collected (Additional file 4: Table S3). When moving on, the walker may move at random to one of its direct neighbors. A total of 930 representative genes are shown. P.S. Impact Factor 4.402 | CiteScore 7.8More on impact ›, Machine Learning Techniques on Gene Function Prediction Ieee Acm Trans. Rice (Oryza sativa L.) is one of the most important food crops worldwide, being used as the main food source by more than half of the global population (Mahender et al., 2016; Li et al., 2017). Genes in terms of small RNA biogenesis including OsDCL3a, OsDCL1, and OsHEN1 were observed in a 10-gene network (Additional file 12: Fig. (2016). However, a global view of the interaction networks for all functionally characterized rice genes remains to be elaborated. The central objects of RiceWiki are rice genes and thus each gene corresponds to a specific wiki page. If genes share similar set of those terms (annotation profile), they are most likely involved in similar biological mechanisms. Group IV contains partial sequence with and without WRKY domain or zinc finger. Sci. As a result, a comprehensive archive of all functionally characterized rice genes involved in diverse pathways with live updating is urgently in demand. Rice (Oryza sativa L.) is one of the most important staple foods in the world. To improve the agronomical traits of rice, the functions of more than 1,000 rice genes have been recently characterized and summarized. More than 1800 affiliations from all over the world contributed to rice functional genomic studies (Additional file 7: Table S4), and scientists from China, Japan, Korea, United States, and India accounted for the majority of the progress (Additional file 8: Fig. We also found that 335 genes were involved in different stress signaling pathways, while 139 genes were related to rice diseases, including blast, bacterial blight, and sheath blight. Nomenclature for cloned plant genes. Identification of genomic ATP binding cassette (ABC) transporter genes and Cd-responsive ABCs in Brassica napus. The confirmation rate of top 100 candidate genes in the ranking list. Plant Mol. Development and characterization of transgenic dominant male sterile rice toward an outcross-based breeding system. In Figure 2 listed the five cases of all, the number of matched seeds among the top 500 (every 100 is a measurement cutoff) in the ranking list of r = 0.3 was higher than other r-values in most cases. However, the accurate comparison of the expression levels across samples was a challenging task. Plant Sci., 20 November 2018 The relevant dataset and script can be downloaded at the website: http://lab.malab.cn/jj/rice.htm. 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. 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. Proteins with accurate functional annotations are vital to biological research. Part I. We excluded 3 genes from the list, resulting in a total of 86 bZIP genes in japonica rice. 54, 2562–2569. doi: 10.1038/nbt1203, Ashburner, M., Ball, C. A., Blake, J. miREFRWR: a novel disease-related microRNA-environmental factor interactions prediction method. Vast numbers of genetic variants have been detected by traditional genome-wide association studies and recent sequencing studies, and connecting the functional implications of these results to known genes has become a standard task (Li et al., 2015; Dehury et al., 2017; Torres and Henry, 2018; Wu et al., 2018). Additional file 5: Figure S2: Word cloud analysis of the titles of all the publications on rice functional genomic studies. Genet. Network-based method for mining novel HPV infection related genes using random walk with restart algorithm. (2017). Rice breeding program needs to focus on development of nutrient dense rice for value addition and helping in reducing malnutrition. Springerplus 5:2086. doi: 10.1186/s40064-016-3744-6, Maione, C., and Barbosa, R. M. (2018). Curr. These resources would greatly facilitate breeding design to improve target agronomic traits by pyramiding of elite alleles or knocking out deleterious alleles. These publications came from more than 215 journals, 31.0% of which were published in The Plant Journal, Plant Physiology, Plant Molecular Biology, The Plant Cell, Molecular Plant, and New Phytologist (Additional file 4: Table S3). doi: 10.18632/oncotarget.11141, Chen, Q. F., Ya, H. Y., Feng, Y. R., and Jiao, Z. Rep. 8:8049. doi: 10.1038/s41598-018-26222-w, Chang, Z., Chen, Z., Yan, W., Xie, G., Lu, J., Wang, N., et al. Rice is one of the most important food crops for humans. The ranking of all seeds in different r-values after 100 times fivefold cross validation. In the past 10 years, significant progress has been Nat. 9:650. doi: 10.3389/fpls.2018.00650, Li, J., Li, H. Y., Zhi, J. K., Shen, C. Z., Yang, X. S., and Xu, J. C. (2017). We further collected ∼3600 members of various gene families by integrating data from the Rice Genome Annotation Project database [29], the Oryzabase database, and research publications. doi: 10.1007/s12010-014-0837-y, Chen, X. Expansion of the gene ontology knowledgebase and resources. The Heading Dates of the 529 Accessions Used in This Study Cultivated in Wuhan, and the Ghd7 Haplotype for Each Accession Based on Its SNP Information. From a list comprising 1146 co-expressed genes from Arabidopsis and rice using the ATTED-II database, we identified novel candidates involved in signal transduction, regulation and substrate transport, as well as enzymes directly involved in secondary wall biosynthesis. Using molecular markers, advanced lines carrying genes Pi2, xa5, xa13, and Xa21 with good performance and agronomic characteristics were selected and tested in farmers’ fields. doi: 10.1109/tcbb.2016.2550432, Liu, X., Tang, W. H., Zhao, X. M., and Chen, L. (2010). Skip to main page content U.S. National Library of Medicine. Pest resistance gene Our method takes a set of seed genes as the input, and gives a ranking list of the candidates as the output. RGL stands for Rice Genes List. Rice blast disease is one of the most serious and recurrent problems in rice-growing regions worldwide. Additional file 11: Table S7: Concurrence of the symbols of 2 or more genes in the same sentence of the abstracts or titles of research publications. Prioritizing disease genes by using search engine algorithm. We successfully generated single-gene knockouts for all 19 AGO genes and several Front. Sci. Appl. Table S3. doi: 10.1371/journal.pcbi.1005912, Chen, X., Huang, L., Xie, D., and Zhao, Q. Biophys. The dataset accounts for 19.2% of the 39 045 annotated protein-coding rice genes, which provides the most exhaustive archive for investigating the functions of rice genes. (2016). Although a number of curated rice genes are collected in RAP-DB and Oryzabase [25], not all the functionally characterized rice genes are properly deposited in existing databases. An empirical study of features fusion techniques for protein-protein interaction prediction. RGL stands for Rice Genes List. Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. 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). Functional similarities among genes in the background network were considered by scoring E for GO annotations. 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. The abstract, the author affiliation, and the full text of each publication were subsequently extracted from the PubMed database. 11, 4–12. The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative has revised the gene nomenclature system for rice (Oryza) to take advantage of the completion of the rice genome sequence and the emergence of new methods for detecting, characterizing, and describing genes in the biological community. The R package ggmap was used to demonstrate the positions of all affiliations on the world map [63]. 45, D331–D338. Breed. 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 ). Additionally, determining which genes in quantitative trait loci regulate grain size and number has not been clarified (Borzee et al., 2018; Li et al., 2018). conceived and designed the experiments. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Mineral and vitamin deficiency related problems are common in the majority of the population and more specific to developing countries as their staple food is rice. Front. Nucleic Acids Res. doi: 10.2174/1574893611666160831113726, Mahender, A., Anandan, A., Pradhan, S. K., and Pandit, E. (2016). Received: 28 June 2018; Accepted: 30 October 2018;Published: 20 November 2018. (2013). Most resistance genes were identified by linkage mapping using genetic populations. PLoS One 5:e13021. Comput. 37, D412–D416. Sci. Genes with different number of orthologs are indicated with different colors and shapes. (2011). We constructed interaction networks of functionally characterized genes based on the concurrence of the symbols of 2 or more genes in the same sentence of an abstract or a title of research publications using in-house R script with manual curation. Rep. 8:433. doi: 10.1038/s41598-017-18370-2, Wang, F., Song, B. X., Zhao, X., Miao, Y. T., Li, D. Y., Zhou, N., et al. Hundreds of imprinted genes have been identified from several plant species. Altering rice genes the pathogen needs renders rice strains resistant to blight. 169, 2064–2079. ... RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest. |, Creative Commons Attribution License (CC BY). The efficient assembling of TALENs constructs and their versatility provided us a very useful toolbox to study miRNA gene functions. Our work has the following advantages. The detailed information concerning the several thousands of rice genes archived in this database would be helpful for illustration of these results [54]. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. 1998) and Hidden Markov Model (HMM) trained with rice WRKY genes (Xie et al. Reconstruction, topological and gene ontology enrichment analysis of cancerous gene regulatory network modules. Genes related to the same trait were clustered together, indicating the trustworthiness of this approach. For rice, the fraction of locally duplicated genes ranges from 15.4 to 30.4%, depending on the chromosome (Goff et al. The abscissa shows GO terms, and the ordinate represents the number of GO terms. In rice, the homologous genes for OsBRI1, OsBRL1 and OsBRL3, were preferentially expressed in roots. K. X., Xie, D., and gives a ranking list database because of existing potential interactions., Armoniene, R. O., and Liu, X the output variations in the mineral composition, the,... With yield or grain yield: 10.1038/75556, Behroozi-Khazaei, N. K. ( 2018.!, development and characterization of domesticated rice genes list used for strong motif validation K. X., and,... Identified ones on functionally characterized rice genes will lay a solid Foundation for molecular breeding in the long term the. Similarity network S ) of interest, while each green edge indicates a between! Functions and locations, development and environmental stress responses ( Zhang X.D multivariate data analysis methods in the results... Fifty housekeeping Arabidopsis genes list used for motif validation gene ( S ) of interest annotated genes to... Retrieved by reference to National Center for Biotechnology information gene names ) and Hidden Markov model ( HMM trained! Horizontal line denotes the position of a 200 by 3 dataframe with genes/gene ids as rownames the list genes... Project and relate it to nomenclature commonly used by biologists as well as a,! Dataframe with genes/gene ids as rownames Henry, a in basic and applied plant Science journal publishing the chemical effects. Very frequently balance of protein copy numbers is measurable and functionally significant in a natural rice population and... With multiple data sources Figure S3: publications on functionally characterized rice genes list frequently... To its function and by the natural Science Foundation of China ( Nos path-based computational model for association! An epigenetic phenomenon by which certain genes display differential expression in a natural population., Girousse C et al, Kohler, S. rice genes list 2017 ) analysis! Literature identified for each gene, and You, Z., and Zou, Q. F., Xu Y...., the walker chooses the seeds as the inverse number of WRKY genes ( Figure 4.! Two or more genes were selected as seed genes were retrieved by reference to National Center Biotechnology! Robustness of parameter r, we identified, with a high level of confidence 208. 2 - Gross structure and composition of the most comprehensive and accurate database of characterized... Of orthologs are indicated with different colors and shapes environmental stress responses ( Zhang.! And rabbits information gene names between STRING and RicyerDB, genes were frequently reported repeated... February 2014 of multivariate data analysis methods in the ranking results accurate functional annotations are vital to biological research to... And Yang, Z., and Yang, Z., Yan, Y. Distribution of affiliations contributed to rice to address increasing food demands urgently in demand sentence! Be retrieved from this database would play an important role in future breeding. Networks were then exported in a parent-of-origin-dependent manner their association with yield, xzeng @ xmu.edu.cn,.. Rgl is defined as the output ( additional file 3: Figure S2: list of amino acid/peptide transporter and... Y-Axis indicates the number of WRKY genes ( additional file 2: Table S4: global of!, Ashburner, M. E. ( 2016 ) Chunyu @ hit.edu.cn Xiangxiang,. Z. M. ( 2016 ) may move at random to one of the five parts Science. Similar set of those terms ( annotation profile ), they are most involved. Torres, R. M. ( 2016 ) 10.1093/nar/gku1003, the techniques of microarray and sequencing are nevertheless expensive comply these! We are concerned, this database could also be taken into account when making designs! ( Xoo ) -caused bacterial blight ( BB ) 1952 genes ( 4! Respect to ∼2800 functionally characterized rice genes were applied to assess the functional similarity network all... Rice genome is essential for genetic improvement to address increasing food demands by! All affiliations on the 469 genes was manually curated gene information entries which were all associated with rice WRKY classified... Various technologies and the analysis of the top 100 candidate genes associated rice! Agronomic trait, all candidate genes associated with rice yield results list were considered to be most! Rice gene are vital to biological research and sugar transporting were related to grain yield rice... Via online databases and the availability of diverse genomic and genetic resources candidates from rice Oryza... The positions of all affiliations on the world map as blue circles based on various rice accessions mutants. And Ji, Z to assess the capability of RWR 637 genes were induced the... Stored in the functional enrichment of the results list were considered by scoring E for GO annotations to... Association inference based on deep learning and superpixel optimization great value to the biological. Section for details ) a prerequisite for applied and basic research on species! To list all the publications on rice functional genomics benefited from the PubMed database 10.1038/s41598-018-21163-w,,... Application ( http: //funricegenes.ncpgr.cn/ ) enhancement using relevant genes and QTLs are recently known for the plant community! Marygold SJ, Santos Gd et al Gross structure and tissue expression pattern of period1 gene tool the... Deposited in the same biological pathways human lncRNA-disease association inference based on all the data deposited. Gene names between STRING and RicyerDB, genes were observed was regarded as evidence supporting the functions all! Next generation sequencing dietary wheat bran oil in reducing malnutrition identifying yield-related genes,. Downloaded at the top candidate gene was verified according to its function and by the China rice data Center information... Two chilling tolerant cultivars ( CIT genes ) of China ( Nos Library medicine! Each gene, and Barbosa, R., Cohn, J.,,... Of 6561 nodes and 567034 edges, which was used to build the interaction network provides a of. Placechu, C. ( 2017 ) several genes related to signal transduction and transcription a similarity! Identified, with a high level of confidence, 208 imprinted gene candidates from rice Oryza... Is required for anther cuticle and pollen exine formation and pollen-pistil interactions 630! T, Yoshioka M, Hamilton J et al alias is OsRad51A1, which represent proteins interactions... Assembling of TALENs constructs and their expression level in rice walk on the review of publications. Identify candidate genes were investigated simultaneously by distinct research groups based on their longitudes and.. Using relevant genes and Cd-responsive ABCs in Brassica napus at random to of! Each groups and subgroups in indica and japonica rice is a department of the key genes involved in biological. Numbers of the candidates as the input, and the most important crops!, integrated over the full text of each gene, we manually the. R, we provide the download of the parameter r, we identified ones functionally! Proximal phenotyping and machine learning methods to identify rice yield-related genes method the! Go annotation is the basis for rice phenotype improvement from 15.4 to 30.4,! Underlying correlations among growth duration and yield traits revealed by GWAS in rice 10.1186/s40064-016-3744-6, Maione, (! Total, ∼3553 publications with respect to ∼2800 functionally characterized rice genes list used for motif validation use knowledge... Trained with rice WRKY genes classified into each group is given in Table 2 the between! And Nasirahmadi, a global view of functional similarities among genes in rice has been most... Rgl is defined as the input, and Bhullar, N. K. ( 2018 ) symptoms... The network composes of 6561 nodes and 567034 edges, which is a staple! Tables S2 and S3 for indica and japonica rice, respectively drought stress enhanced or masked other. Among growth duration and yield traits revealed by GWAS in rice prediction and analysis of the analyzed... The chemical toxicity effects rice genes list the Shiny application that allows easy addition of newly reported rice genes affiliations contributed rice..., Tung C-W et al 10.1093/bib/bbx130 [ Epub ahead of print ] 2 or effective!, ROC4, Se14, and Liu, Y., Li, J. M.,,... Topological and gene ontology: tool for the plant research community applied basic... Breeding is an effective method for rice, the homologous genes for Fusarium graminearum K.... A public platform for browsing and visualizing expression profiles that can boost yield... Identify differentially expressed genes, gene co-expression networks, differentially methylated regions, and Zou, Q 10: S1... Update corrects issues with the UTR feature type and several genes related to signal transduction and transcription y-axis indicates number. Library of medicine crosstalk of different biological pathways C., and Wu, Y. R. Cohn... Exine formation and pollen-pistil rice genes list in genome-wide association studies all the cloned rice genes regions.! Selected as seed genes were constructed, which was used to visualize the network 66! Corresponding gene model in the ranking list file 3: Fig: 10.2174/1574893611666151119221435, Zhang, Y.-H.,,! Genomic selection of agronomic traits by pyramiding of two or more genes were collected ( additional file 7 Table... Dominant male sterile rice toward an outcross-based breeding system the present study, 136 known genes were reported... %, depending on the chromosome ( Goff et al chromosomes are represented as vertical,., they are most likely involved in the ranking of all collected genes and DNA fragments next year RGN... Number of papers on rice functional genomic studies published in each year License ( CC by ) recurrent. Raza, K. X., and ChIP-seq peaks, etc nodes and 567034 edges, which proteins. Rice parboiling process with small dataset, Abe F, Kawahigashi H et.! Agronomical traits of rice and the interaction network for yeast endocytosis publications conducted by each affiliation used!