PlantEMS is an integrative database designed for the storage, analysis, and visualization of DNA, RNA, and protein PTM (post-translational modification) sites in plants. It includes the experimental-confirmed modification datasets from published literatures and existing databases, covering 54 plant species. Specifically, the PlantEMS database collected 13,009,568 DNA modification sites for 4 types from 6 plants; 33,337 RNA modification sites for 28 types from 33 plants; and 132,232 PTM sites for 25 types from 28 plants (Fig 1.).

Fig 1. The overview of PlantEMS

The home page is displayed in the following Fig 2-1 and Fig 2-2:

Fig 2-1:

• The main functions of the database are provided in menu bar form (boxed in red).
• Introduction and overview of PlantEMS.
• Major genera quick start for PlantEMS. Click on image to get the basic information and overview of the plant (Fig 2-2).
• The news and updates of PlantEMS.

Fig 2-1. Home page

Fig 2-2:

The basic information and overview of the plant.

Fig 2-2. Home page

In browse page, users can access the information about various types of modifications for different plant species.

Fig 3-1:

Select the omics level of modification.

Fig 3-1. Browse page

Fig 3-2:

Example for browsing DNA page.

• Select species and modification types.
• View major information including data sources, sequencing techniques, feature distribution, data quality, and other details for different modifications. Click each button for specific information.
• The corresponding information in 2.

Fig 3-2. Browse page

PlantEMS offers a variety of search methods to help users retrieve specific query results. For DNA and RNA queries, available search options include ‘Search by Gene’, ‘Search by Position’, ‘Search by Modification Type’, and ‘Search by ID’. For PTM queries, the methods provided are ‘Search by Species’, ‘Search by Peptide’, ‘Search by Accession’, ‘Search by Modification Type’, and ‘Search by ID’.

Fig 4-1:

Select the omics level of modification.

Fig 4-1. Search page

Fig 4-2:

Example for searching DNA page.

• Select species, modification type and gene name.
• Example of this search method.
• Click ‘Search’ button for query result.
• The function introduction and parameter explanation.

Fig 4-2. Search page for DNA by gene

Fig 4-3:

Example for searching DNA page.

• Select species, chromosome, modification type, the start and end position on the chromosome.
• Example of this search method.
• Click ‘Search’ button for query result.
• The function introduction and parameter explanation.

Fig 4-3. Search page for DNA by position

Fig 4-4:

Example for searching DNA page.

• Select modification type.
• Example of this search method.
• Click ‘Search’ button for query result.
• The function introduction and parameter explanation.

Fig 4-4. Search page for DNA by modification type

Fig 4-5:

Example for searching DNA page.

• Select ID.
• Example of this search method.
• Click ‘Search’ button for query result.
• The function introduction and parameter explanation.

Fig 4-5. Search page for DNA by ID

Fig 4-6:

Example for searching PTM page.

Fig 4-6. Search page for PTM

In the result page, each entry is displayed with essential details such as species, chromosome, position, type, gene etc.

Fig 5-1:

Example for search result page in DNA.

• Select columns to display.
• Query information and query result.
• Click to link to graphical user interface with integrated genome browser for visualization of aligned reads and regions of interests.
• Click to turn the page.
• Click to return search page.

Fig 5-1. Search result page for DNA

Fig 5-2:

Example for search result page in PTM.

• Select columns to display.
• Query information and query result.
• Click to link to the Uniprot database for more information.
• Click to turn the page.
• Click to return search page.

Fig 5-2. Search result page for PTM

The Prediction tool provides 13 omics-types-species predictions in our database, including DNA-4mC-C. equisetifolia, DNA-4mC-F. Vesca, DNA-6mA-A. thaliana, DNA-6mA-C. equisetifolia, DNA-6mA-F. Vesca, DNA-6mA-R. Chinensis, RNA-m5C-A. thaliana, PTM-2-hydroxyisobutyrylation-O. sativa, PTM-acetylation-O. sativa, PTM-crotonylation-O. sativa, PTM-malonylation-O. sativa, PTM-succinylation-O. sativa, PTM-ubiquitination-O. sativa.

Fig 6-1:

Select the omics level of modification.

Fig 6-1. Tools page

Fig 6-2:

Prediction tool page in DNA.

• Introduction and usage for prediction tool.
• Choose modification types and species.
• Directly input one or more DNA sequences or upload a fasta file with FASTA format.
• To submit/get example/clear.

Fig 6-2. Tools page for DNA

Fig 7-1:

Example for prediction tool result page in DNA.

• The predicted results.
• To download/continue.

Fig 7-1. Prediction tool result page for DNA

Fig 8-1:

Select the omics level of modification.

Fig 8-1. Download page

Fig 8-2:

Select the species and click to download the interested data.

Fig 8-2. Download page