Single cell type - SCRN2 - The Human Protein Atlas

SCRN2

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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.	SCRN2
Gene descriptionⁱ Full gene name according to HGNC.	Secernin 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes
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.	5

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.	Proximal tubular cells - Amino acid metabolism (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.	Group enriched (Proximal tubular cells, Proximal enterocytes)
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.	0.46
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: Group enriched (Proximal tubular cells, Proximal enterocytes)

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

SCRN2 is part of cluster 56 Proximal tubular cells - Amino acid metabolism with confidenceⁱ 1
204 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.
BDH2	3-hydroxybutyrate dehydrogenase 2	0.8741	56
ACY3	Aminoacylase 3	0.8392	56
SLC7A13	Solute carrier family 7 member 13	0.8331	56
SLC6A18	Solute carrier family 6 member 18	0.8258	56
PDZK1	PDZ domain containing 1	0.8215	38
TMEM174	Transmembrane protein 174	0.8179	56
BPHL	Biphenyl hydrolase like	0.8118	56
MT1F	Metallothionein 1F	0.8095	56
MT1H	Metallothionein 1H	0.8014	56
FMO4	Flavin containing dimethylaniline monoxygenase 4	0.7971	56
MIOX	Myo-inositol oxygenase	0.7969	56
SLC6A13	Solute carrier family 6 member 13	0.7966	56
CTXN3	Cortexin 3	0.7934	56
RBP5	Retinol binding protein 5	0.7902	56
AGMAT	Agmatinase	0.7884	56

IMMUNE CELLS

SCRN2 is part of cluster 45 Eosinophils - Unknown function with confidenceⁱ 0.98
257 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.
PPID	Peptidylprolyl isomerase D	0.9762	45
HNRNPUL1	Heterogeneous nuclear ribonucleoprotein U like 1	0.9762	45
RNF11	Ring finger protein 11	0.9762	45
MIEF2	Mitochondrial elongation factor 2	0.9524	45
TM7SF3	Transmembrane 7 superfamily member 3	0.9524	45
ARMC10	Armadillo repeat containing 10	0.9524	45
CPNE2	Copine 2	0.9524	45
CIDEB	Cell death inducing DFFA like effector b	0.9524	45
ENSG00000284976	Novel RING finger protein	0.9286	22
PPP1R26	Protein phosphatase 1 regulatory subunit 26	0.9286	29
PRKRIP1	PRKR interacting protein 1	0.9286	22
FBXL12	F-box and leucine rich repeat protein 12	0.9048	45
C19orf25	Chromosome 19 open reading frame 25	0.9048	36
TRIM62	Tripartite motif containing 62	0.9048	45
R3HCC1	R3H domain and coiled-coil containing 1	0.9048	45

Adipocytes	23.1 nTPM
Adipose tissue	24.3 nTPM
Breast	21.8 nTPM

Alveolar cells type 1	10.7 nTPM
Lung	10.7 nTPM

Alveolar cells type 2	16.1 nTPM
Lung	16.1 nTPM

Astrocytes	14.2 nTPM
Brain	14.2 nTPM

B-cells	18.1 nTPM
Kidney	41.6 nTPM
PBMC	24.6 nTPM
Lung	24.1 nTPM
Bone marrow	21.5 nTPM
Skin	18.6 nTPM
Lymph node	17.6 nTPM
Spleen	16.3 nTPM
Thymus	14.3 nTPM
Stomach	13.9 nTPM
Salivary gland	12.8 nTPM
Esophagus	11.8 nTPM
Liver	9.7 nTPM
Adipose tissue	8.6 nTPM

Ciliated cells	32.0 nTPM
Bronchus	48.2 nTPM
Fallopian tube	39.6 nTPM
Lung	23.4 nTPM
Endometrium	16.9 nTPM

Club cells	33.4 nTPM
Bronchus	57.0 nTPM
Prostate	26.0 nTPM
Lung	17.2 nTPM

Endothelial cells	23.1 nTPM
Placenta	56.2 nTPM
Ovary	37.0 nTPM
Testis	35.1 nTPM
Esophagus	30.1 nTPM
Skeletal muscle	26.6 nTPM
Heart muscle	26.2 nTPM
Skin	26.2 nTPM
Fallopian tube	23.2 nTPM
Thymus	22.6 nTPM
Tongue	21.3 nTPM
Breast	18.5 nTPM
Pancreas	15.5 nTPM
Vascular	15.5 nTPM
Lung	14.4 nTPM
Endometrium	14.1 nTPM
Prostate	12.6 nTPM
Salivary gland	12.5 nTPM
Liver	8.8 nTPM

Enteroendocrine cells	39.5 nTPM
Small intestine	51.5 nTPM
Colon	35.2 nTPM
Rectum	31.9 nTPM

Fibroblasts	25.7 nTPM
Placenta	44.8 nTPM
Esophagus	38.8 nTPM
Adipose tissue	35.7 nTPM
Salivary gland	34.2 nTPM
Breast	27.9 nTPM
Liver	27.3 nTPM
Fallopian tube	25.9 nTPM
Heart muscle	25.5 nTPM
Skeletal muscle	25.4 nTPM
Stomach	24.5 nTPM
Skin	21.4 nTPM
Thymus	20.0 nTPM
Pancreas	18.5 nTPM
Vascular	15.9 nTPM
Prostate	13.2 nTPM
Lung	11.7 nTPM

Granulocytes	28.8 nTPM
Tongue	34.0 nTPM
Lung	30.3 nTPM
Fallopian tube	22.1 nTPM

Intestinal goblet cells	34.5 nTPM
Small intestine	49.4 nTPM
Rectum	29.2 nTPM
Colon	25.1 nTPM

Lymphatic endothelial cells	27.0 nTPM
Ovary	32.7 nTPM
Fallopian tube	21.2 nTPM

Macrophages	11.6 nTPM
Kidney	26.6 nTPM
Bone marrow	16.2 nTPM
Spleen	16.0 nTPM
Pancreas	14.4 nTPM
Fallopian tube	14.0 nTPM
Esophagus	12.8 nTPM
Testis	12.4 nTPM
Adipose tissue	10.7 nTPM
Prostate	10.6 nTPM
Lung	10.5 nTPM
Thymus	10.5 nTPM
Stomach	10.3 nTPM
Skeletal muscle	10.0 nTPM
Tongue	8.7 nTPM
Breast	8.7 nTPM
Skin	7.8 nTPM
Salivary gland	7.3 nTPM
Vascular	6.9 nTPM
Endometrium	6.8 nTPM

Paneth cells	41.0 nTPM
Colon	50.7 nTPM
Rectum	37.9 nTPM
Small intestine	34.5 nTPM

Basal prostatic cells	17.1 nTPM
Prostate	17.1 nTPM

Basal respiratory cells	40.0 nTPM
Bronchus	40.0 nTPM

Basal squamous epithelial cells	24.4 nTPM
Esophagus	24.4 nTPM

Bipolar cells	10.8 nTPM
Eye	10.8 nTPM

Plasma cells	29.6 nTPM
Stomach	51.5 nTPM
Esophagus	31.2 nTPM
Thymus	30.8 nTPM
Fallopian tube	30.6 nTPM
Salivary gland	27.3 nTPM
Liver	24.0 nTPM
Bone marrow	22.7 nTPM
Spleen	18.8 nTPM

Schwann cells	22.3 nTPM
Esophagus	47.9 nTPM
Vascular	10.4 nTPM
Adipose tissue	8.6 nTPM

Serous glandular cells	19.2 nTPM
Salivary gland	20.7 nTPM
Tongue	17.7 nTPM

Smooth muscle cells	17.6 nTPM
Placenta	41.0 nTPM
Adipose tissue	31.6 nTPM
Ovary	27.6 nTPM
Fallopian tube	21.4 nTPM
Liver	20.4 nTPM
Skin	20.3 nTPM
Skeletal muscle	14.9 nTPM
Esophagus	14.4 nTPM
Lung	14.1 nTPM
Salivary gland	13.1 nTPM
Thymus	12.8 nTPM
Breast	12.8 nTPM
Tongue	12.6 nTPM
Prostate	9.7 nTPM
Vascular	8.5 nTPM
Endometrium	7.0 nTPM

Suprabasal keratinocytes	13.6 nTPM
Tongue	15.7 nTPM
Skin	11.6 nTPM

T-cells	17.8 nTPM
Kidney	34.6 nTPM
Colon	30.2 nTPM
PBMC	28.9 nTPM
Liver	28.7 nTPM
Bone marrow	27.7 nTPM
Spleen	19.2 nTPM
Fallopian tube	19.0 nTPM
Skeletal muscle	18.5 nTPM
Stomach	18.4 nTPM
Lymph node	17.8 nTPM
Adipose tissue	17.0 nTPM
Lung	14.2 nTPM
Thymus	13.6 nTPM
Vascular	12.9 nTPM
Salivary gland	12.4 nTPM
Esophagus	12.2 nTPM
Skin	11.6 nTPM
Endometrium	11.4 nTPM
Prostate	9.5 nTPM
Tongue	9.2 nTPM
Breast	7.5 nTPM

Undifferentiated cells	39.3 nTPM
Small intestine	55.2 nTPM
Rectum	33.6 nTPM
Colon	29.0 nTPM

Amygdala excitatory	11.9 nTPM
Basal ganglia	16.1 nTPM
Cerebral cortex	12.9 nTPM
Hippocampus	12.0 nTPM
Thalamus	10.9 nTPM
Amygdala	9.8 nTPM
Hypothalamus	9.5 nTPM

Astrocyte	21.3 nTPM
Cerebral cortex	26.6 nTPM
Pons	25.4 nTPM
Medulla oblongata	24.0 nTPM
Hippocampus	23.9 nTPM
Cerebellum	23.6 nTPM
Midbrain	22.2 nTPM
Spinal cord	21.3 nTPM
Thalamus	21.3 nTPM
Basal ganglia	18.2 nTPM
Amygdala	14.1 nTPM
Hypothalamus	13.8 nTPM

Bergmann glia	16.2 nTPM
Pons	21.6 nTPM
Cerebellum	18.5 nTPM
Medulla oblongata	8.5 nTPM

Central nervous system macrophage	11.7 nTPM
Cerebellum	15.0 nTPM
Spinal cord	14.1 nTPM
Cerebral cortex	13.7 nTPM
Hippocampus	13.7 nTPM
Pons	12.0 nTPM
Midbrain	11.9 nTPM
Medulla oblongata	11.0 nTPM
Thalamus	10.5 nTPM
Amygdala	9.7 nTPM
Basal ganglia	9.5 nTPM
Hypothalamus	7.3 nTPM

Cerebellar inhibitory	15.8 nTPM
Cerebellum	18.9 nTPM
Midbrain	17.4 nTPM
Pons	15.5 nTPM
Spinal cord	13.7 nTPM
Medulla oblongata	13.6 nTPM

Cge interneuron	12.1 nTPM
Cerebral cortex	15.0 nTPM
Midbrain	14.2 nTPM
Basal ganglia	13.1 nTPM
Hippocampus	12.8 nTPM
Amygdala	10.7 nTPM
Hypothalamus	9.5 nTPM
Thalamus	9.4 nTPM

Choroid plexus epithelial cell	17.3 nTPM
Thalamus	19.2 nTPM
Medulla oblongata	18.6 nTPM
Hippocampus	16.6 nTPM
Basal ganglia	14.9 nTPM

Committed oligodendrocyte precursor	11.2 nTPM
Basal ganglia	13.1 nTPM
Cerebellum	12.7 nTPM
Pons	12.4 nTPM
Midbrain	11.8 nTPM
Medulla oblongata	11.6 nTPM
Spinal cord	11.0 nTPM
Hippocampus	10.9 nTPM
Amygdala	10.7 nTPM
Hypothalamus	10.2 nTPM
Cerebral cortex	9.5 nTPM
Thalamus	9.5 nTPM

Deep-layer corticothalamic and 6b	11.9 nTPM
Midbrain	15.5 nTPM
Hippocampus	14.2 nTPM
Basal ganglia	13.0 nTPM
Cerebral cortex	13.0 nTPM
Amygdala	8.2 nTPM
Hypothalamus	7.4 nTPM

Deep-layer intratelencephalic	9.8 nTPM
Basal ganglia	12.8 nTPM
Cerebral cortex	12.1 nTPM
Amygdala	8.8 nTPM
Hippocampus	8.1 nTPM
Hypothalamus	7.2 nTPM

Deep-layer near-projecting	20.8 nTPM
Basal ganglia	25.2 nTPM
Cerebral cortex	24.0 nTPM
Amygdala	21.4 nTPM
Hippocampus	19.8 nTPM
Hypothalamus	13.5 nTPM

Eccentric medium spiny neuron	15.3 nTPM
Basal ganglia	18.1 nTPM
Hypothalamus	16.4 nTPM
Cerebral cortex	15.9 nTPM
Thalamus	14.7 nTPM
Amygdala	14.2 nTPM
Hippocampus	12.4 nTPM

Endothelial cell	15.9 nTPM
Medulla oblongata	20.5 nTPM
Cerebellum	19.4 nTPM
Thalamus	19.2 nTPM
Amygdala	19.0 nTPM
Midbrain	18.0 nTPM
Spinal cord	17.3 nTPM
Hippocampus	16.0 nTPM
Pons	13.7 nTPM
Basal ganglia	13.0 nTPM
Cerebral cortex	12.1 nTPM
Hypothalamus	6.2 nTPM