Single cell type - CRIM1 - 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.	CRIM1
Gene descriptionⁱ Full gene name according to HGNC.	Cysteine rich transmembrane BMP regulator 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Transporters
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, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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.	Endothelial cells - Angiogenesis & vascular homeostasis (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 (Podocytes, Endometrial glandular cells, Epicardial cells, Vascular smooth muscle 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.	0.44
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 (Endothelial cell, Vascular associated smooth muscle cell)
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.	Immune cell enhanced (plasmacytoid DC)
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 (nCPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. * Single nuclei Read more
Single cell type groups RNA single cell type group specificity: Cell type enhanced (Renal nephron cells, Glandular 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 (Endothelial cell, Vascular associated smooth muscle cell)

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: Immune cell enhanced (plasmacytoid DC)
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

CRIM1 is part of cluster 12 Endothelial cells - Angiogenesis & vascular homeostasis with confidenceⁱ 1
216 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.
PTPN14	Protein tyrosine phosphatase non-receptor type 14	0.5729	51
MYOF	Myoferlin	0.5718	51
NUAK1	NUAK family kinase 1	0.5716	12
MET	MET proto-oncogene, receptor tyrosine kinase	0.5491	51
TEAD1	TEA domain transcription factor 1	0.5427	51
SMAD6	SMAD family member 6	0.5278	12
ARHGEF12	Rho guanine nucleotide exchange factor 12	0.5265	46
MAP4K3	Mitogen-activated protein kinase kinase kinase kinase 3	0.5264	51
ARHGAP29	Rho GTPase activating protein 29	0.5199	12
RIMKLB	Ribosomal modification protein rimK like family member B	0.5191	51
WWTR1	WW domain containing transcription regulator 1	0.4948	12
FEZ2	Fasciculation and elongation protein zeta 2	0.4947	83
TEK	TEK receptor tyrosine kinase	0.4945	12
LRRC1	Leucine rich repeat containing 1	0.4917	12
PAEP	Progestagen associated endometrial protein	0.4886	51

IMMUNE CELLS

CRIM1 is part of cluster 5 Non-specific - Cell proliferation with confidenceⁱ 0.52
689 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.
ENSG00000276302	Novel protein	1.0000	5
ANKRD13D	Ankyrin repeat domain 13D	1.0000	5
HS6ST1	Heparan sulfate 6-O-sulfotransferase 1	1.0000	5
TXNL4A	Thioredoxin like 4A	1.0000	5
TM9SF3	Transmembrane 9 superfamily member 3	0.9762	5
RCC1L	RCC1 like	0.9762	41
PINLYP	Phospholipase A2 inhibitor and LY6/PLAUR domain containing	0.9762	5
FAM24B	Family with sequence similarity 24 member B	0.9762	5
ZBTB33	Zinc finger and BTB domain containing 33	0.9762	5
MANF	Mesencephalic astrocyte derived neurotrophic factor	0.9762	5
RRP36	Ribosomal RNA processing 36	0.9762	10
IFT43	Intraflagellar transport 43	0.9762	5
CSNK2A2	Casein kinase 2 alpha 2	0.9762	41
BUD13	BUD13 homolog	0.9524	10
CHD1L	Chromodomain helicase DNA binding protein 1 like	0.9524	41