Document manuals

SHOGoiN stores various types of cell-related data associated to cells. On the top page of SHOGoiN, there are several entrances to acquire types of data in addition to a free-text search box. Here, we provide an example of how to retrieve information of a specific cell type.

Example: B cell

    1. Put a keyword 'immune' in the search box after selecting 'Cell Taxonomy (Human)' menu that is located on the top right of SHOGoiN home page, and click [magnifying glass] button.


    2. On 'SHOGoiN Cell Taxonomy' of a result page (display of a list of immune cell types), click [1] in the 'Number' column to display the integration page.


    3. On the integration page for B cell, the user can obtain various types of data associated to B cell. For example,

    • - SHOGoiN Cell Taxonomy provides general profile information associated with B cells such as germ layer, differentiation status, source age, anatomical location, and cell type.
    • - SHOGoiN Cell Transcriptome provides single-cell transcriptome assay data and metadata.
    • - SHOGoiN Cell Conversion provides literature-curated cell differentiation and transdifferentiation information.
    • - SHOGoiN Marker provides literature-curated cell type marker information (marker molecule name, molecular type; gene, protein etc., subcellular location, link to UniProt, gene ID).
    • - Image provides cell images clipped from tissue images and morphological analysis data.
    • - Orthologous Cell provides literature-curated information about orthologous cell types among different species.


    4. Furthermore, by clicking a SOM heatmap on 'SHOGoiN Cell Transcriptome', the user can jump to a page that provides gene marker module data as 'Top 10 up-regulated' and 'Bottom-10 down-regulated' gene tables in addition to a list of genes in a selected area of a histogram or a SOM heatmap.


    5. By clicking a cell image on 'Cell Image', the user can jump to a page that provides detailed information of image assay, morphological analysis data of the selected cell image, and also the original tissue image used to clip the cell image.


    6. On 'SHOGoiN Cell Marker', the data table provides names of marker molecules, cell type information, molecular type; gene, protein etc., subcellular location, link to UniProt, gene ID, and reference information. Those provided information has been collected by Ph.D. curators from commercially available biological products from seven biological companies and the literature.