Single cell type - CR1 - The Human Protein Atlas

GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	CR1
Gene descriptionⁱ Full gene name according to HGNC.	Complement C3b/C4b receptor 1 (Knops blood group)
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Blood group antigen proteins CD markers Plasma proteins
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	6

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.	Neutrophils - Degranulation (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Cell type enhanced (Kupffer cells, Macrophages, B-cells, Monocytes, Erythroid cells, Hofbauer cells)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.89
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Cell type enhanced (Leukocyte, Oligodendrocyte, Fibroblast)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Group enriched (basophil, eosinophil, neutrophil)
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

Single cell type

Cell type enrichment

Single nuclei - Brain

Immune cells

Expression clustering

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types RNA single cell type specificity: Cell type enhanced (Kupffer cells, Macrophages, B-cells, Monocytes, Erythroid cells, Hofbauer cells)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Leukocyte, Oligodendrocyte, Fibroblast)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Group enriched (basophil, eosinophil, neutrophil)
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

CR1 is part of cluster 74 Neutrophils - Degranulation with confidenceⁱ 1
174 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
TLR1	Toll like receptor 1	0.8271	74
TLR6	Toll like receptor 6	0.7977	74
CEACAM4	CEA cell adhesion molecule 4	0.7830	74
NCF4	Neutrophil cytosolic factor 4	0.7640	74
PEAK3	PEAK family member 3	0.7590	74
TLR4	Toll like receptor 4	0.7584	74
FPR1	Formyl peptide receptor 1	0.7560	74
SIGLEC14	Sialic acid binding Ig like lectin 14	0.7486	29
GCA	Grancalcin	0.7482	74
VNN2	Vanin 2	0.7435	74
DOK3	Docking protein 3	0.7265	74
HCLS1	Hematopoietic cell-specific Lyn substrate 1	0.7003	58
LILRB3	Leukocyte immunoglobulin like receptor B3	0.6967	74
P2RY13	Purinergic receptor P2Y13	0.6855	58
ARL11	ADP ribosylation factor like GTPase 11	0.6844	74

IMMUNE CELLS

CR1 is part of cluster 20 Non-specific - DNA binding with confidenceⁱ 0.93
266 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
ATP6V0D2	ATPase H+ transporting V0 subunit d2	1.0000	20
ZNF713	Zinc finger protein 713	1.0000	20
NMNAT3	Nicotinamide nucleotide adenylyltransferase 3	0.9762	20
DNASE1	Deoxyribonuclease 1	0.9762	20
MAN2A2	Mannosidase alpha class 2A member 2	0.9762	20
ZNF493	Zinc finger protein 493	0.9762	20
SLC38A3	Solute carrier family 38 member 3	0.9762	35
RHD	Rh blood group D antigen	0.9762	35
ZNF397	Zinc finger protein 397	0.9762	20
TLCD2	TLC domain containing 2	0.9762	20
TMEM154	Transmembrane protein 154	0.9762	20
ALOX5	Arachidonate 5-lipoxygenase	0.9762	20
TRIM58	Tripartite motif containing 58	0.9762	20
PEBP4	Phosphatidylethanolamine binding protein 4	0.9762	20
OSER1	Oxidative stress responsive serine rich 1	0.9762	20