MyNutRiceBase Tutorial

Sitemap of MyNutRiceBase database. There are six menus for users to explore in the MyNutRiceBase database.

Figure 1. Sitemap of MyNutRiceBase database

1. Search for putative SNPs data associated with flavonoid and folate biosynthetic genes

In the ‘Genotype’ sub-menu under the ‘Genome’ and ‘RNA-seq’ menus, users can query the putative SNPs associated with the flavonoid and folate biosynthetic genes by providing the SNP ID or by filtering the pathway name and the chromosome numbers from the drop-down box (Figure 2). Users can download the results in Excel or CSV format.

An interface in the ‘Genotype’ sub-menu under the ‘RNA-seq’ menu, where users can query the putative SNPs associated with the biosynthetic pathways by providing the SNP ID or by filtering the pathway name and the chromosome numbers from the drop-down box.

2. Search for general putative SNPs panel among pigmented and white rice varieties

‘Other’ sub-menu under ‘Genome’ and ‘RNA-seq’ menu provides users to mine genome-SNPs and expression-SNPs identified among Bali, PH9, MRM16, MRQ100, MR297 and MRQ76 varieties. Users can select SNPs with polymorphic alleles and chromosome based on drop down list button.

3. Search for SNPs panel based on Marker ID, flavonoid genes and polymorphic alleles

‘Markers’ sub-menu under ‘Genome’ menu provides users a list of validated SNPs associated with flavonoid genes. There are 40 pigmented rice varieties that have been genotyped with these validated SNPs. Users can retrieve the validated SNPs by filtering the Marker ID, biosynthetic genes and SNP alleles.

4. Search for annotated SNPs based on SNPs effect or gene ID or SNP ID

Users can retrieve annotated SNPs by providing gene ID (OsID) and SNP ID or by filtering the SNP effects. The ‘SNPs annotation’ sub-menu is available under ‘Genome’ and ‘RNA-seq’ menu.

5. Search for biosynthetic genes based on pathway name, gene ID and gene abbreviation

To retrieve list of flavonoid and folate biosynthetic genes, users can click the ‘Biosynthetic Genes’ sub-menu under ‘Genome’ menu. Users can query the biosynthetic genes  by providing the gene ID or by filtering the pathway name or gene abbreviation.

6. Search for co-expressed genes based on gene ID, transcription factors, PCC values and pathway name

 ‘Co-expressed genes’ sub-menu provides the users with list of co-expressed flavonoid and folate genes with transcription factors and hub genes. Users can retrieve a list of co-expressed genes by filtering the transcription factors, PCC values cut-off and pathway names. The users also can import the list co-expressed genes into Cytoscape software.

7. Finding SNPs based on specific rice varieties

Use ‘Rice Varieties’ sub-menu to retrieve SNPs based on specific rice varieties or to compare the SNPs between rice varieties. Multiple options can be selected under Varieties, Gene abbreviation, Gene Symbol, SNP effects and chromosome.