Browse tree
Cell types with available cell markers are underlined
| Cell type | #Species | #Tissues | #Conditions | #Cell markers | #Publications |
|---|---|---|---|---|---|
| Cell Taxonomy ID | Cell type | Cell Ontology ID | Tissue ID | Tissue |
|---|---|---|---|---|
- Myeloid dendritic cell, human
- Myeloid dendritic cell, human is distributed in .
- For Myeloid dendritic cell, human, there are conserved cell markers whose orthologs are also reported as cell markers for this cell type.
- The relevant cell markers of Myeloid dendritic cell, human are ranked in terms of supported literature, expression enrichment and conservation.
-
Show valueNo. of publications>=log2FCThe median log2 fold-change of expression (FDR < 0.05) in a cell cluster to that in all other cells among the available scRNA-seq samples>=Highly expressed ratioNumber of samples in which genes are more highly expressed in this cell type compared to other cell types (log2FC > 0.25, FDR < 0.05) divided by number of total samples for the cell type>=Specificity scoreThe median cell specificity score (calculated by Jensen-Shannon divergence score, ranging from 0 to 1) among available scRNA-seq samples>=Conservation scoreNumber of ortholog genes which are also reported as cell markers for this cell type in other species>=
Total
Show publication-supported cell markers
Show publication-supported cell markers or rank cell markers by the y-axis value
Rank by highly expressed ratio
No results
| Cell marker | No. of total samples (E) | No. of highly expressed samples (HE, FDR<0.05) | Highly expressed ratio (HE/E) |
|---|
| Species | Sample | Condition | Cell marker | log2FC |
Pct.cell type
The expression percentage of this gene in this cell type
|
Pct.others
The expression percentage of this gene in other cell types
|
P value | FDR |
|---|
No results
| Species | Sample | Condition | Cell marker |
Cell specificity score
Jensen-Shannon (JS) divergence score (0-1) is calculated to quantify the cell type specificity of one cell marker (Cabili MN et al., 2011 ).
|
|---|
| Cell marker | No. of publications |
FDR
The FDR is calculated by fisher’s exact test to see if this cell marker is specifically associated with this cell type by publication.
|
Species | Evidence | Antibody | Protein class |
|---|
- For Myeloid dendritic cell, human, the similarity of reported cell marker composition between different species is shown below.
| Species in comparison | Tissue |
Cell-type similarity across species
The cell-type similarity across species is evaluated by the number of orthologous cell markers divided by the union of cell markers in the two species
|
No. of orthologous cell markers |
|---|
- The conserved cell markers and their orthologous genes which are also reported as cell markers for the same cell type are showed below.
| Cell marker | Species (ortholog) | Ortholog | Gene ID (ortholog) | No. of publications (ortholog cell markers) |
|---|
| Species | Tissue | Cell type in comparison |
Marker similarity score
The similarity score (0-1) is calculated between two cell types by the number of common markers normalized by union of marker set sizes. One represents the same marker sets of two cell types and zero means the two cell types share no common markers.
|
|---|---|---|---|
Set the filters of cell number, ROGUE, silhouette coefficient, and their averaged estimates by adjusting the hover cursors of the legends.
Cell number
Top
100%
ROGUE index
Top
100%
Average ROGUE index
Top
100%
Silhouette coefficient
Top
100%
Average Silhouette coefficient
Top
100%
| Species | Accession number | Sample | PMID | Cell number |
ROGUE index
ROGUE is calculated to accurately quantify the purity of identified cell clusters. A ROGUE value greater than 0.9 indicates a cell cluster with high purity.
|
Silhouette coefficient
The Silhouette coefficient ranges from -1 to 1, and 1 means clusters are well apart from each other, 0 means clusters are indifferent, and -1 means clusters are defined in the wrong way.
|
Average ROGUE index
Mean ROGUE index of all cell clusters in the sample.
|
Average silhouette coefficient
Mean silhouette coefficient of all cell clusters in the sample.
|
|---|