![Page 1: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/1.jpg)
Comprehensive understanding and application of
rice functional genes
funRiceGenes
![Page 2: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/2.jpg)
Part I
Display of information in this database as static web pages
https://funricegenes.github.io/
![Page 3: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/3.jpg)
https://funricegenes.github.io/
At the homepage of ourdatabase, we provide thedownload of the wholedataset in tidy format.
On-site search usingGoogle or Bing
![Page 4: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/4.jpg)
The GENE menu lists 2900+cloned rice genes.
The detailed information of agene is shown as a single page.
Link to MSU
Link to RAPdb
Link to PubMedLink to GenBank
Link to PubMed
https://funricegenes.github.io/
![Page 5: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/5.jpg)
Link to MSU Link to RAPdb
Link to PubMed
https://funricegenes.github.io/
The FAMS menu lists 400+rice gene families.
The detailed information of agene family is shown as asingle page.
![Page 6: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/6.jpg)
https://funricegenes.github.io/
The KEYS menu lists allkeywords regardingphenotype description orbiological process.
Each keyword links to a listof genes related to thiskeyword.
![Page 7: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/7.jpg)
The NEWS menu shows the updatinghistory of this database.
https://funricegenes.github.io/
![Page 8: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/8.jpg)
https://funricegenes.github.io/
The DOCS menu lists all theliteratures archived in this database.
Link to PubMed
![Page 9: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/9.jpg)
At the homepage of our database, we provide a link toa website allowing interactive query of this database.
https://funricegenes.github.io/
![Page 10: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/10.jpg)
Interactive query of this database
http://funricegenes.ncpgr.cn/
Part II
![Page 11: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/11.jpg)
The Gene menu allows query of 2900+ genes using a MSU/RAPdbgenomic locus or a gene symbol.
Detail information of a geneare shown in different tables
http://funricegenes.ncpgr.cn/
Link to MSULink to RAPdb
![Page 12: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/12.jpg)
Detail information of a geneare shown in different tables
http://funricegenes.ncpgr.cn/
The GeneFamily menu allows query of 5000+ gene family membersusing a MSU/RAPdb genomic locus or a gene symbol.
Link to MSULink to RAPdb
![Page 13: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/13.jpg)
http://funricegenes.ncpgr.cn/
Link to MSULink to RAPdb Link to PubMed
The Keyword menu allows query of the database with keywordsregarding phenotype description or biological process.
![Page 14: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/14.jpg)
The Publication menu allows query of the titles and abstractsof all publications archived in this database with any word.
http://funricegenes.ncpgr.cn/
![Page 15: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/15.jpg)
http://funricegenes.ncpgr.cn/
The IDConversion menu provides a tool to convert between a MSUgenomic locus and a RAPdb genomic locus.
Batch query is supported.
![Page 16: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/16.jpg)
http://funricegenes.ncpgr.cn/
The IDConversion menu also provides a tool to convert betweenindica and japonica gene IDs.
Batch query is supported.
Link to RAPdbLink to MSU Link to http://rice.hzau.edu.cn/rice/
![Page 17: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/17.jpg)
http://funricegenes.ncpgr.cn/
The Download menu provides extractingof gene information using MSU genomiclocus or RAPdb genomic locus.
![Page 18: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/18.jpg)
http://funricegenes.ncpgr.cn/
Our database provides tools allowing submissionof new information.
Currently, only our team members havepermissions to submit new information.
![Page 19: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/19.jpg)
Link to https://funricegenes.github.io/
http://funricegenes.ncpgr.cn/
![Page 20: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/20.jpg)
Add new records to this database
http://funricegenes.ncpgr.cn/
Part III
![Page 21: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/21.jpg)
Daily email alert from PubMed
![Page 22: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/22.jpg)
We identified a PubMed record (24723033) from the email alert, which describedthe cloning of a rice gene (OsGT47A).
We further identified the genomic locus LOC_Os01g70190 and Os01g0926600assigned by the MSU and the RAPdb database by manually searching of the full textof this paper at https://link.springer.com/article/10.1007%2Fs10265-014-0631-5.
One record in PubMedhttps://www.ncbi.nlm.nih.gov/pubmed/24723033
![Page 23: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/23.jpg)
Then go tohttp://funricegenes.ncpgr.cn/
In the Gene menu, fill in the four cells “GeneSymbol”, “MSU genomic locus”, “RAPdb genomiclocus” and “Pubmed ID” and click “Submit”.
The Shiny application will extract informationon this gene from the publication and add allthe information to this database.
![Page 24: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/24.jpg)
Now, gene OsGT47A isincluded in this database!
New info added successfully!Once succeeded, the Shiny application will give a popup message
![Page 25: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/25.jpg)
If the paper on the cloning of a new gene was not archived in PubMed, we can useother functionality of the Shiny application to submit this gene to thefunRiceGenes database.
Submit basic information of the gene.
Submit publication on the gene.
Other approaches
![Page 26: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/26.jpg)
Deploy the Shiny application on local computer
Part IV
![Page 27: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/27.jpg)
The content of the Shiny application (http://funricegenes.ncpgr.cn/)was deposited in Github (https://github.com/venyao/RICENCODE).You can deploy the Shiny application on local computer.
Before running the app you will need to have R and RStudio installed(tested with R 3.3.3 and RStudio 1.0.143).
Please check CRAN (https://cran.r-project.org/) for theinstallation of R.
Please check https://www.rstudio.com/ for the installation ofRStudio.
Step 1: Install R and Rstudio
![Page 28: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/28.jpg)
Start an R session using RStudio and run these lines:# try http:// if https:// URLs are not supportedinstall.packages("shiny") install.packages("shinythemes") install.packages("shinyBS") install.packages("RCurl") install.packages("XML") install.packages("stringr") install.packages("plyr")
Step 2: Install the R Shiny package and other packages required by the Shiny application
![Page 29: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/29.jpg)
Go to https://github.com/venyao/RICENCODEDownload the content of the Shiny application as a ZIP file.
Step 3: Download the content of theShiny application
![Page 30: funRiceGenes · Symbol”, “MSU genomic locus”, “RAPdb genomic locus” and “Pubmed ID” and click “Submit”. The Shiny application will extract information on this gene](https://reader033.vdocument.in/reader033/viewer/2022050305/5f6e31c42d69d9438342d314/html5/thumbnails/30.jpg)
Unzip the ZIP file in Step 3 into a directory (for example, /RICENCODE/).Start an R session using RStudio and run these lines:library(shiny)runApp(“/RICENCODE/”, launch.browser = TRUE)The first parameter of runApp is the directory where the content of this Shinyapplication is stored. In this directory, you can find two R scripts server.R and ui.R.
Then your browser will open theShiny application.
Step 4: Launch the Shiny application