CellKb Immune

CellKb Immune provides manually curated marker gene sets and literature-derived cell-type matches to support assignment of hematopoietic immune cell types from single-cell RNA sequencing (scRNA-seq) data in mammalian systems, with a focus on mouse models.

Key Features:

• Manually Curated Marker Gene Sets: Marker gene sets are compiled from peer-reviewed scientific literature to represent a wide range of immune cell types.
• Comprehensive Ontological Annotation: Each gene set is annotated with ontologies for cell type, tissue origin, and associated diseases to provide biological context.
• Single-Cell RNA Sequencing Support: The database is intended for assignment of cell types based on scRNA-seq gene expression profiles.
• Gene-List Matching Search Methodology: The search method accepts input gene lists and returns matching immune cell type signatures derived from the literature.
• Validation and Reliability: Contents and search capabilities have been evaluated using a leave-one-out approach and validated by annotating marker gene sets from bulk RNA-seq datasets.

Scientific Applications:

• Single-Cell Transcriptomics Annotation: Assigning and interpreting cell types in scRNA-seq datasets focused on immune and hematopoietic populations.
• Immune Response Studies: Characterizing dynamics and composition of immune cell populations during immune responses.
• Disease Modeling: Linking specific immune cell types to pathological conditions for mechanistic studies.
• Translational Research: Supporting development of targeted therapies by providing precise immune cell type annotations.

Methodology:

Marker gene sets were manually compiled from peer-reviewed literature; ontological annotations for cell type, tissue, and disease were integrated; a literature-based search matches input gene lists to marker gene sets; performance was evaluated using a leave-one-out approach and validated by annotating marker gene sets from bulk RNA-seq datasets.