Supporting data for "funRiceGenes dataset for comprehensive understanding and application of rice functional genes"

Dataset type: Genomic, Software
Data released on November 08, 2017

Yao W; Li G; Yu Y; Ouyang Y (2017): Supporting data for "funRiceGenes dataset for comprehensive understanding and application of rice functional genes" GigaScience Database. http://dx.doi.org/10.5524/100375

DOI10.5524/100375

As a main staple food, rice is also a model plant for functional genomics researches of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address the increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement. We built a comprehensive and accurate dataset of ~2,800 functionally characterized rice genes and ~5,000 members of different gene families, by integrating data from available database and review of every publication of rice functional genomics researches. 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. We also constructed 214 gene interaction networks based on 1,841 connections between 1,310 genes. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. Increasing degree of conservation of the flowering pathway was identified among closer related plants, implying substantial value for rice genes in future dissection of flowering regulation in other crops. All data are deposited in the funRiceGenes database (https://funricegenes.github.io/), with interactive query and continuous updating using a Shiny application (http://funricegenes.ncpgr.cn/).

Additional details

Read the peer-reviewed publication(s):

Yao, W., Li, G., Yu, Y., & Ouyang, Y. (2017). funRiceGenes dataset for comprehensive understanding and application of rice functional genes. GigaScience, 7(1). doi:10.1093/gigascience/gix119

Additional information:

https://funricegenes.github.io/

https://github.com/funRiceGenes/funRiceGenes.github.io

https://github.com/venyao/RICENCODE

http://funricegenes.ncpgr.cn/





File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive8.5 MB2017-11-01
ReadmeTEXT2.3 KB2017-11-01
Github archivearchive28.8 MB2017-11-01
R scriptszip227 KB2017-11-01
Displaying 1-4 of 4 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China Y Ouyang 31371599
National Natural Science Foundation of China 31771873
National Key Technology R&D Program of China 2016YFD0100903
National Program for Support of Top-notch Young Professionals This project belongs to the "National Program for Special Support of Eminent Professionals".
Date Action
November 16, 2017 Dataset publish
November 16, 2017 File RICENCODE-master.zip updated
November 16, 2017 File R-scripts.zip updated
November 16, 2017 File readme.txt updated
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix119