Single cell type - NRGN - The Human Protein Atlas

NRGN

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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.	NRGN
Gene descriptionⁱ Full gene name according to HGNC.	Neurogranin
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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.	Platelets - Hemostasis (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 (Excitatory neurons, Alveolar cells type 2, Smooth muscle cells, Monocytes)
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.	0.75
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.	Low cell type specificity
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.	Low immune cell specificity
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 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 (Excitatory neurons, Alveolar cells type 2, Smooth muscle cells, Monocytes)

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: Low cell type specificity

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: Low immune cell specificity
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

NRGN is part of cluster 57 Platelets - Hemostasis with confidenceⁱ 1
173 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.
TUBB1	Tubulin beta 1 class VI	0.8467	57
LY6G6F	Lymphocyte antigen 6 family member G6F	0.8458	57
PF4	Platelet factor 4	0.8453	57
PPBP	Pro-platelet basic protein	0.8453	57
GP9	Glycoprotein IX platelet	0.8446	57
RGS18	Regulator of G protein signaling 18	0.8431	57
TREML1	Triggering receptor expressed on myeloid cells like 1	0.8413	57
OR2B6	Olfactory receptor family 2 subfamily B member 6	0.8383	57
RUFY1	RUN and FYVE domain containing 1	0.8370	57
GP1BA	Glycoprotein Ib platelet subunit alpha	0.8364	57
TRAPPC3L	Trafficking protein particle complex subunit 3L	0.8286	57
MAP3K7CL	MAP3K7 C-terminal like	0.8266	57
PF4V1	Platelet factor 4 variant 1	0.8248	57
MMD	Monocyte to macrophage differentiation associated	0.8220	57
SCGB1C1	Secretoglobin family 1C member 1	0.8213	57

IMMUNE CELLS

NRGN is part of cluster 7 Non-specific - Innate immune response with confidenceⁱ 1
237 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.
TOLLIP	Toll interacting protein	1.0000	7
ENSG00000289690	Novel transcript	1.0000	7
ODF3B	Outer dense fiber of sperm tails 3B	1.0000	7
SLC43A2	Solute carrier family 43 member 2	1.0000	7
GIT2	GIT ArfGAP 2	1.0000	7
RAB5C	RAB5C, member RAS oncogene family	1.0000	7
IMPDH1	Inosine monophosphate dehydrogenase 1	1.0000	7
SMNDC1	Survival motor neuron domain containing 1	0.9762	7
TUBGCP3	Tubulin gamma complex associated protein 3	0.9762	7
FGL2	Fibrinogen like 2	0.9762	7
RAB20	RAB20, member RAS oncogene family	0.9762	7
IMPA2	Inositol monophosphatase 2	0.9762	7
PAK1	P21 (RAC1) activated kinase 1	0.9762	7
CDC123	Cell division cycle 123	0.9762	7
SHISA5	Shisa family member 5	0.9762	7

Adipocytes	12.0 nTPM
Breast	16.7 nTPM
Adipose tissue	7.3 nTPM

Alveolar cells type 1	4.5 nTPM
Lung	4.5 nTPM

Alveolar cells type 2	97.1 nTPM
Lung	97.1 nTPM

Astrocytes	34.1 nTPM
Brain	34.1 nTPM

B-cells	2.9 nTPM
PBMC	26.2 nTPM
Liver	4.8 nTPM
Thymus	1.9 nTPM
Skin	1.7 nTPM
Adipose tissue	0.8 nTPM
Lymph node	0.8 nTPM
Salivary gland	0.8 nTPM
Spleen	0.2 nTPM
Kidney	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	2.9 nTPM
Fallopian tube	5.7 nTPM
Lung	4.8 nTPM
Endometrium	1.2 nTPM
Bronchus	0.1 nTPM

Club cells	1.2 nTPM
Lung	2.7 nTPM
Prostate	0.8 nTPM
Bronchus	0.1 nTPM

Endothelial cells	19.0 nTPM
Placenta	50.5 nTPM
Ovary	47.4 nTPM
Endometrium	46.9 nTPM
Fallopian tube	33.7 nTPM
Skin	26.7 nTPM
Lung	22.7 nTPM
Esophagus	13.8 nTPM
Testis	13.7 nTPM
Pancreas	12.9 nTPM
Breast	12.3 nTPM
Thymus	11.9 nTPM
Vascular	11.5 nTPM
Prostate	9.4 nTPM
Tongue	8.6 nTPM
Skeletal muscle	7.5 nTPM
Salivary gland	6.3 nTPM
Liver	5.0 nTPM
Heart muscle	0.6 nTPM

Enteroendocrine cells	3.3 nTPM
Rectum	8.4 nTPM
Colon	1.6 nTPM
Small intestine	0.0 nTPM

Fibroblasts	2.8 nTPM
Pancreas	12.2 nTPM
Lung	6.1 nTPM
Vascular	6.1 nTPM
Stomach	5.8 nTPM
Liver	3.6 nTPM
Breast	3.3 nTPM
Fallopian tube	1.8 nTPM
Thymus	1.7 nTPM
Skeletal muscle	0.9 nTPM
Prostate	0.7 nTPM
Salivary gland	0.7 nTPM
Skin	0.5 nTPM
Adipose tissue	0.4 nTPM
Placenta	0.2 nTPM
Esophagus	0.1 nTPM
Heart muscle	0.0 nTPM

Granulocytes	1.6 nTPM
Lung	3.0 nTPM
Fallopian tube	1.7 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	1.3 nTPM
Colon	2.0 nTPM
Rectum	1.1 nTPM
Small intestine	0.8 nTPM

Lymphatic endothelial cells	9.7 nTPM
Ovary	16.4 nTPM
Fallopian tube	3.0 nTPM

Macrophages	27.0 nTPM
Skeletal muscle	71.4 nTPM
Adipose tissue	67.8 nTPM
Kidney	53.1 nTPM
Bone marrow	46.6 nTPM
Stomach	38.6 nTPM
Fallopian tube	37.3 nTPM
Spleen	28.1 nTPM
Endometrium	27.7 nTPM
Testis	25.4 nTPM
Thymus	22.9 nTPM
Vascular	17.9 nTPM
Breast	13.3 nTPM
Lung	12.8 nTPM
Skin	12.3 nTPM
Esophagus	11.6 nTPM
Pancreas	8.2 nTPM
Salivary gland	7.5 nTPM
Tongue	7.0 nTPM
Prostate	3.4 nTPM

Paneth cells	0.3 nTPM
Rectum	1.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Distal tubular cells	3.1 nTPM
Kidney	3.1 nTPM

Plasma cells	2.9 nTPM
Esophagus	10.4 nTPM
Liver	5.0 nTPM
Thymus	2.6 nTPM
Spleen	1.7 nTPM
Fallopian tube	1.6 nTPM
Bone marrow	1.5 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM

Schwann cells	1.5 nTPM
Vascular	2.6 nTPM
Adipose tissue	2.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.2 nTPM
Salivary gland	0.4 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	71.2 nTPM
Breast	219.7 nTPM
Ovary	214.4 nTPM
Esophagus	127.3 nTPM
Thymus	90.8 nTPM
Adipose tissue	75.9 nTPM
Fallopian tube	73.0 nTPM
Prostate	56.0 nTPM
Lung	55.3 nTPM
Skin	53.3 nTPM
Salivary gland	50.3 nTPM
Vascular	48.9 nTPM
Endometrium	20.3 nTPM
Skeletal muscle	18.4 nTPM
Tongue	17.4 nTPM
Liver	16.6 nTPM
Placenta	2.5 nTPM

T-cells	3.1 nTPM
PBMC	28.8 nTPM
Skeletal muscle	16.6 nTPM
Lung	3.9 nTPM
Liver	3.3 nTPM
Endometrium	1.7 nTPM
Skin	1.4 nTPM
Breast	1.2 nTPM
Fallopian tube	1.1 nTPM
Colon	1.0 nTPM
Spleen	1.0 nTPM
Kidney	0.9 nTPM
Tongue	0.9 nTPM
Adipose tissue	0.8 nTPM
Vascular	0.8 nTPM
Lymph node	0.7 nTPM
Thymus	0.7 nTPM
Prostate	0.2 nTPM
Salivary gland	0.2 nTPM
Bone marrow	0.1 nTPM
Stomach	0.1 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	6.2 nTPM
Colon	11.8 nTPM
Rectum	4.2 nTPM
Small intestine	2.6 nTPM

Amygdala excitatory	150.3 nTPM
Thalamus	211.0 nTPM
Amygdala	183.4 nTPM
Basal ganglia	165.2 nTPM
Cerebral cortex	138.1 nTPM
Hippocampus	131.6 nTPM
Hypothalamus	72.2 nTPM

Astrocyte	8.3 nTPM
Cerebral cortex	36.2 nTPM
Hippocampus	13.0 nTPM
Basal ganglia	11.1 nTPM
Hypothalamus	10.5 nTPM
Amygdala	9.3 nTPM
Thalamus	4.3 nTPM
Midbrain	2.8 nTPM
Pons	1.5 nTPM
Medulla oblongata	1.3 nTPM
Spinal cord	0.8 nTPM
Cerebellum	0.0 nTPM

Bergmann glia	0.0 nTPM
Cerebellum	0.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	13.6 nTPM
Cerebral cortex	72.3 nTPM
Hippocampus	30.1 nTPM
Amygdala	15.8 nTPM
Basal ganglia	9.6 nTPM
Hypothalamus	9.1 nTPM
Thalamus	5.3 nTPM
Medulla oblongata	2.2 nTPM
Midbrain	1.9 nTPM
Spinal cord	1.8 nTPM
Pons	1.7 nTPM
Cerebellum	0.1 nTPM

Cerebellar inhibitory	2.2 nTPM
Pons	4.7 nTPM
Midbrain	4.4 nTPM
Medulla oblongata	1.7 nTPM
Cerebellum	0.4 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	12.2 nTPM
Cerebral cortex	20.5 nTPM
Hippocampus	16.2 nTPM
Amygdala	13.9 nTPM
Basal ganglia	12.9 nTPM
Hypothalamus	11.5 nTPM
Midbrain	5.9 nTPM
Thalamus	4.6 nTPM

Choroid plexus epithelial cell	6.5 nTPM
Hippocampus	19.4 nTPM
Thalamus	5.5 nTPM
Medulla oblongata	0.9 nTPM
Basal ganglia	0.4 nTPM

Committed oligodendrocyte precursor	22.1 nTPM
Basal ganglia	60.8 nTPM
Cerebral cortex	48.8 nTPM
Hypothalamus	41.0 nTPM
Amygdala	36.1 nTPM
Hippocampus	26.4 nTPM
Midbrain	10.9 nTPM
Medulla oblongata	7.7 nTPM
Thalamus	6.5 nTPM
Spinal cord	3.7 nTPM
Pons	1.8 nTPM
Cerebellum	0.0 nTPM

Deep-layer corticothalamic and 6b	290.7 nTPM
Midbrain	380.5 nTPM
Cerebral cortex	372.7 nTPM
Basal ganglia	355.6 nTPM
Amygdala	265.4 nTPM
Hippocampus	207.9 nTPM
Hypothalamus	161.8 nTPM

Deep-layer intratelencephalic	327.5 nTPM
Cerebral cortex	442.3 nTPM
Basal ganglia	352.1 nTPM
Hippocampus	344.2 nTPM
Hypothalamus	264.6 nTPM
Amygdala	234.3 nTPM

Deep-layer near-projecting	316.7 nTPM
Hippocampus	528.8 nTPM
Cerebral cortex	370.8 nTPM
Amygdala	275.2 nTPM
Basal ganglia	252.0 nTPM
Hypothalamus	156.5 nTPM

Eccentric medium spiny neuron	386.2 nTPM
Basal ganglia	505.2 nTPM
Thalamus	503.5 nTPM
Hippocampus	465.9 nTPM
Hypothalamus	290.8 nTPM
Cerebral cortex	283.8 nTPM
Amygdala	268.1 nTPM

Endothelial cell	14.3 nTPM
Cerebral cortex	49.2 nTPM
Amygdala	27.9 nTPM
Hippocampus	20.5 nTPM
Hypothalamus	16.1 nTPM
Basal ganglia	15.8 nTPM
Midbrain	8.5 nTPM
Pons	5.6 nTPM
Medulla oblongata	5.1 nTPM
Thalamus	5.1 nTPM
Spinal cord	1.7 nTPM
Cerebellum	1.5 nTPM

Ependymal cell	7.0 nTPM
Hippocampus	17.3 nTPM
Amygdala	11.4 nTPM
Hypothalamus	10.7 nTPM
Basal ganglia	9.5 nTPM
Midbrain	7.6 nTPM
Thalamus	5.3 nTPM
Pons	0.8 nTPM
Medulla oblongata	0.7 nTPM
Spinal cord	0.0 nTPM