POCT database manual
1. Home page
The home page provides an introduction to the POCT. It explains that POCT is a curated classification system for plant cell types, which helps in organizing, exploring, and comparing cell identities across different species and developmental contexts. There are two main classification trees in POCT: the tissue - oriented tree and the cell - type - oriented tree.
Additionally, the home page has a search section where you can search for cell types across these two classification trees. You can enter tissue or cell type names in the corresponding search forms and click the search buttons to get relevant results.
2. Tissue-oriented tree page
This page displays a tree structure of tissue-classified POCT data. It allows you to view the hierarchical relationships, cell type definitions, and attribute information of different tissues and cell types.
You can use the search bar at the top to search for specific tissue or cell type names. When you enter a query, the system will highlight the matching nodes in the tree. If a match is found, the tree will expand all the parent nodes of the matching node, and the page will scroll to the location of the first matching node.
Clicking on a node in the tree will show detailed information about that node on the right - hand side, including its name, label, Chinese name, path, Plant Ontology ID, POCT ID, definition, and combined levels.
3. Cell-type-oriented tree page
Similar to the tissue-oriented tree page, this page presents a cell-type-classified POCT data tree. The cell tree groups the cell type entries in the tissue tree according to their cell identities.
There is also a search function. You can search for cell types using keywords such as guard cell or POCT_ID. When a search is performed, the matching nodes will be highlighted, and the relevant parent nodes will be expanded. The page will then scroll to the first matching node.
By default, the page shows the details of the "Epidermis" node. Clicking on any node in the tree will display its detailed information, including name, label, Plant Ontology ID, POCT ID, definition, and combined levels.
4. MarkerDB page
The MarkerDB Page provides access to the PlantscRNAdb database, a comprehensive resource for cell type-specific marker genes in plants. This database is essential for researchers seeking to explore the molecular signatures of various plant cell types. It includes detailed information on marker gene expression patterns, functions, and associated pathways.
On this page, you can search for marker genes using criteria such as gene names, cell types, or species. Search results provide comprehensive details for each marker gene, including its sequence, expression levels across different tissues and developmental stages, and known regulatory elements.
Additionally, the MarkerDB Page offers tools for visualizing gene expression data, such as heatmaps and scatter plots, to help identify patterns and relationships among marker genes. You can also download marker gene data in various formats for further analysis and access links to related databases for complementary resources.
5. Download page
On this page, you can download the POCT data files. There are two types of data available: POCT Tissue - oriented Tree Data and POCT Celltype - oriented Tree Data.
Each type of data is presented in a card. Clicking the "Download" button in each card will allow you to download the corresponding data in XLSX format. The data includes cell type definitions, hierarchical relationships, and attribute information.
6. Consortium page
The Consortium Page provides information about the collaborative efforts behind the POCT project. It lists the institutions, research groups, and key individuals involved in the consortium. You can find details about their roles, contributions, and areas of expertise.
7. Release notes page
This page provides information about the cell tree construction. It mentions that the cell tree groups cell type terms from the tissue tree according to cell identities, with the first level being cell identities and the subsequent levels corresponding to specific cell type terms in the tissue tree.
There are also some metadata statistics, such as the number of cell type records, the maximum level, the number of cell properties, and the number of terms at different levels. In addition, a list of references used in the project is provided.
8. Contact page
If you have any questions, suggestions, or concerns about the POCT project, you can use this page to contact the POCT team. There are two ways to communicate: offline and online.
For offline communication, you can visit the Institute of Crop Science & Institute of Bioinformatics at Zhejiang University, located at 866 Yuhangtang Road, Hangzhou, Zhejiang Province, China 310058.
For online communication, you can send an email to bioinplant@zju.edu.cn or hongyuchen@zju.edu.cn.