Tool:CellKb 2.0: A database of cell type marker gene sets

Question

[Ashwini Patil]

CellKb - a database of cell type markers

CellKb is a knowledgebase of cell type marker gene sets manually collected from scientific literature and annotated with cell, tissue and disease ontologies.

Contents

• 22,568 marker gene sets
• 1,802 cell types
• 403 publications
• 11 species

The cell type markers are taken primarily from tables, figures or supplementary materials/websites of publications describing single-cell RNA-seq experiments and select bulk RNA-seq and microarray experiments from public databases. More about data collection, curation and annotation in CellKb.

CellKb 2.0 FREE academic version

With this version, users can:

• Search cell types using one or more genes (identified using a variation of the Rank Bias Overlap algorithm)
• Get a list of top 20 matching genes between query gene list and matching cell types
• Search cell types by keywords such a disease, cell type ontology, sample condition
• Browse all cell types by various categories such as species, disease, publication year, tissue and cell type name

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CellKb 2.0 screenshots

1. Find matching cell types using a query gene list

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2. List of matching cell types

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3. Overlapping query genes within matching cell type

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4. Search cell types matching a keyword

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5. List of cell types having keyword

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6. Browse CellKb categories

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7. See cell types within category

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8. View cell types in a publication

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[Ashwini Patil]

CellKb Immune, a database of immune cell type marker gene sets from mouse, is available at https//www.cellkb.com/immune

CellKb Immune is free for academic users.