CellMarker 2.0

CellMarker 2.0 provides a manually curated database of experimentally supported cell-type markers across human and mouse tissues and computational modules for analyzing single-cell sequencing data.

Key Features:

• Manually curated, experimentally supported markers: Contains experimentally validated markers collected through manual curation for human and mouse cell types.
• Extensive database expansion: Adds 36,300 tissue–cell type–marker entries (covering 474 tissues, 1,901 cell types, and 4,566 markers) for a total of 83,361 entries, 26,915 cell markers, 2,578 cell types, and 656 tissues.
• Diverse sequencing sources: Integrates marker information from 48 sequencing technology sources, including 10X Chromium, Smart-Seq2, and Drop-seq.
• Broadened marker types: Incorporates 29 additional marker types, including long non-coding RNAs (lncRNAs) and processed pseudogenes, alongside protein-coding genes.
• Analysis modules: Provides computational modules for cell annotation, cell clustering, cell malignancy detection, cell differentiation analysis, cell feature analysis, and cell communication analysis.

Scientific Applications:

• Identification of novel cell types: Enabling discovery of previously unrecognized cell populations using the expanded marker repertoire.
• Cancer research: Supporting malignancy detection and characterization of cancerous versus non-malignant cells.
• Developmental biology: Facilitating analysis of cellular differentiation pathways and lineage relationships.
• Single-cell transcriptomics: Supporting analyses that leverage diverse sequencing technologies (e.g., 10X Chromium, Smart-Seq2, Drop-seq) for high-resolution cellular profiling in human and mouse.

Methodology:

Manual curation of experimentally supported markers and integration of marker data from 48 sequencing technologies (e.g., 10X Chromium, Smart-Seq2, Drop-seq), with computational modules for cell annotation, clustering, malignancy detection, differentiation analysis, feature analysis, and cell communication analysis.