Single cell type - SHE - The Human Protein Atlas

SHE

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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.	SHE
Gene descriptionⁱ Full gene name according to HGNC.	Src homology 2 domain containing E
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.	3

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.	Adipocytes & Endothelial cells - Mixed function (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 (Endothelial cells, Adipocytes, Lymphatic endothelial cells, Spermatocytes, Microglial cells, Kupffer cells, Alveolar cells type 1)
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.	0.80
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 enriched (Endothelial 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.	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 (Endothelial cells, Adipocytes, Lymphatic endothelial cells, Spermatocytes, Microglial cells, Kupffer cells, Alveolar cells type 1)

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 enriched (Endothelial 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: 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

SHE is part of cluster 41 Adipocytes & Endothelial cells - Mixed function with confidenceⁱ 1
325 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.
RAMP3	Receptor activity modifying protein 3	0.8265	41
ROBO4	Roundabout guidance receptor 4	0.8064	41
SCARF1	Scavenger receptor class F member 1	0.7533	41
CCL14	C-C motif chemokine ligand 14	0.7463	41
CCL23	C-C motif chemokine ligand 23	0.7400	41
IL33	Interleukin 33	0.7352	41
FAM167B	Family with sequence similarity 167 member B	0.7273	41
GIMAP8	GTPase, IMAP family member 8	0.7177	41
EGFL7	EGF like domain multiple 7	0.7169	41
TEK	TEK receptor tyrosine kinase	0.7113	41
FCN3	Ficolin 3	0.7027	41
LIFR	LIF receptor subunit alpha	0.6970	41
PCDH12	Protocadherin 12	0.6835	41
CDH5	Cadherin 5	0.6816	41
TAOK2	TAO kinase 2	0.6748	41

IMMUNE CELLS

SHE is part of cluster 8 Plasmacytoid DCs - Unknown function with confidenceⁱ 0.66
236 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.
TMEM98	Transmembrane protein 98	1.0000	8
ABCA2	ATP binding cassette subfamily A member 2	0.9762	8
ENSG00000286264	Novel protein	0.9762	8
KLRF2	Killer cell lectin like receptor F2	0.9762	8
ZNF888	Zinc finger protein 888	0.9762	8
SPRED2	Sprouty related EVH1 domain containing 2	0.9762	8
PDILT	Protein disulfide isomerase like, testis expressed	0.9762	30
PLAC8	Placenta associated 8	0.9762	8
BRME1	Break repair meiotic recombinase recruitment factor 1	0.9762	8
IRF2BPL	Interferon regulatory factor 2 binding protein like	0.9762	30
ABCB6	ATP binding cassette subfamily B member 6 (Langereis blood group)	0.9762	8
YPEL1	Yippee like 1	0.9762	8
EPDR1	Ependymin related 1	0.9762	8
LLGL2	LLGL scribble cell polarity complex component 2	0.9762	8
TOP2B	DNA topoisomerase II beta	0.9524	8

Adipocytes	52.9 nTPM
Breast	55.2 nTPM
Adipose tissue	50.6 nTPM

Alveolar cells type 1	21.5 nTPM
Lung	21.5 nTPM

Alveolar cells type 2	18.9 nTPM
Lung	18.9 nTPM

Astrocytes	3.7 nTPM
Brain	3.7 nTPM

B-cells	0.5 nTPM
Skin	3.4 nTPM
Thymus	1.8 nTPM
Spleen	0.4 nTPM
Stomach	0.4 nTPM
Lymph node	0.3 nTPM
Salivary gland	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	0.7 nTPM
Fallopian tube	1.7 nTPM
Lung	0.9 nTPM
Endometrium	0.3 nTPM
Bronchus	0.0 nTPM

Club cells	0.4 nTPM
Lung	0.5 nTPM
Prostate	0.5 nTPM
Bronchus	0.1 nTPM

Endothelial cells	75.5 nTPM
Skeletal muscle	112.0 nTPM
Testis	111.4 nTPM
Liver	109.6 nTPM
Esophagus	103.1 nTPM
Thymus	98.9 nTPM
Vascular	89.5 nTPM
Heart muscle	85.7 nTPM
Salivary gland	80.8 nTPM
Prostate	79.5 nTPM
Lung	78.8 nTPM
Placenta	67.0 nTPM
Breast	66.8 nTPM
Fallopian tube	64.8 nTPM
Tongue	62.1 nTPM
Endometrium	49.8 nTPM
Skin	39.4 nTPM
Ovary	37.1 nTPM
Pancreas	23.3 nTPM

Enteroendocrine cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	11.5 nTPM
Liver	88.9 nTPM
Stomach	15.9 nTPM
Skin	13.1 nTPM
Skeletal muscle	9.1 nTPM
Thymus	9.0 nTPM
Adipose tissue	7.8 nTPM
Salivary gland	7.4 nTPM
Breast	5.5 nTPM
Heart muscle	5.3 nTPM
Vascular	5.3 nTPM
Esophagus	4.4 nTPM
Lung	4.1 nTPM
Fallopian tube	3.8 nTPM
Prostate	3.3 nTPM
Pancreas	0.3 nTPM
Placenta	0.2 nTPM

Granulocytes	8.5 nTPM
Lung	15.1 nTPM
Fallopian tube	5.6 nTPM
Tongue	4.9 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	44.2 nTPM
Fallopian tube	50.3 nTPM
Ovary	38.2 nTPM

Macrophages	4.9 nTPM
Skin	23.4 nTPM
Vascular	14.4 nTPM
Esophagus	11.6 nTPM
Thymus	11.3 nTPM
Skeletal muscle	6.4 nTPM
Adipose tissue	4.5 nTPM
Tongue	3.8 nTPM
Fallopian tube	3.6 nTPM
Stomach	2.6 nTPM
Prostate	2.2 nTPM
Salivary gland	2.2 nTPM
Spleen	2.0 nTPM
Breast	1.3 nTPM
Testis	1.2 nTPM
Endometrium	1.2 nTPM
Kidney	0.9 nTPM
Lung	0.9 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM

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

Early spermatids	12.4 nTPM
Testis	12.4 nTPM

Plasma cells	3.2 nTPM
Esophagus	20.8 nTPM
Liver	3.5 nTPM
Fallopian tube	0.6 nTPM
Thymus	0.4 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM

Schwann cells	3.4 nTPM
Adipose tissue	5.5 nTPM
Vascular	4.7 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.7 nTPM
Salivary gland	1.4 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	8.0 nTPM
Liver	89.2 nTPM
Skeletal muscle	18.7 nTPM
Tongue	6.3 nTPM
Breast	1.6 nTPM
Thymus	1.5 nTPM
Fallopian tube	1.5 nTPM
Skin	1.4 nTPM
Salivary gland	1.3 nTPM
Esophagus	1.2 nTPM
Prostate	1.2 nTPM
Vascular	1.2 nTPM
Placenta	0.7 nTPM
Adipose tissue	0.7 nTPM
Ovary	0.6 nTPM
Endometrium	0.2 nTPM
Lung	0.0 nTPM

T-cells	0.4 nTPM
Vascular	2.8 nTPM
Skeletal muscle	1.5 nTPM
Liver	1.2 nTPM
Salivary gland	0.6 nTPM
Lung	0.5 nTPM
Skin	0.4 nTPM
Breast	0.4 nTPM
Endometrium	0.1 nTPM
Adipose tissue	0.1 nTPM
Bone marrow	0.1 nTPM
Stomach	0.1 nTPM
Thymus	0.1 nTPM
Tongue	0.1 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Spleen	0.0 nTPM
Prostate	0.0 nTPM

Undifferentiated cells	0.0 nTPM
Rectum	0.1 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Amygdala excitatory	0.8 nTPM
Hippocampus	2.2 nTPM
Cerebral cortex	1.0 nTPM
Thalamus	0.5 nTPM
Hypothalamus	0.4 nTPM
Amygdala	0.3 nTPM
Basal ganglia	0.3 nTPM

Astrocyte	5.1 nTPM
Amygdala	10.3 nTPM
Cerebral cortex	9.0 nTPM
Hippocampus	8.7 nTPM
Basal ganglia	7.2 nTPM
Midbrain	5.3 nTPM
Hypothalamus	5.0 nTPM
Thalamus	3.8 nTPM
Pons	2.8 nTPM
Cerebellum	1.8 nTPM
Medulla oblongata	1.8 nTPM
Spinal cord	0.7 nTPM

Bergmann glia	2.0 nTPM
Medulla oblongata	4.3 nTPM
Cerebellum	1.8 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	9.0 nTPM
Amygdala	16.5 nTPM
Hippocampus	13.5 nTPM
Cerebral cortex	12.6 nTPM
Basal ganglia	10.9 nTPM
Hypothalamus	8.6 nTPM
Midbrain	7.7 nTPM
Cerebellum	7.6 nTPM
Thalamus	7.3 nTPM
Pons	5.9 nTPM
Medulla oblongata	5.8 nTPM
Spinal cord	2.9 nTPM

Cerebellar inhibitory	0.2 nTPM
Medulla oblongata	0.6 nTPM
Cerebellum	0.3 nTPM
Pons	0.2 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	1.0 nTPM
Basal ganglia	1.7 nTPM
Hypothalamus	1.6 nTPM
Cerebral cortex	1.2 nTPM
Amygdala	1.1 nTPM
Hippocampus	1.1 nTPM
Thalamus	0.5 nTPM
Midbrain	0.2 nTPM

Choroid plexus epithelial cell	0.1 nTPM
Basal ganglia	0.3 nTPM
Medulla oblongata	0.3 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.4 nTPM
Midbrain	1.7 nTPM
Cerebral cortex	1.3 nTPM
Hypothalamus	0.7 nTPM
Basal ganglia	0.5 nTPM
Hippocampus	0.5 nTPM
Thalamus	0.2 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	0.2 nTPM
Hippocampus	0.3 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.2 nTPM
Hypothalamus	0.2 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.3 nTPM
Basal ganglia	0.5 nTPM
Amygdala	0.3 nTPM
Hypothalamus	0.3 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM

Deep-layer near-projecting	0.2 nTPM
Amygdala	0.4 nTPM
Basal ganglia	0.3 nTPM
Cerebral cortex	0.3 nTPM
Hypothalamus	0.2 nTPM
Hippocampus	0.0 nTPM

Eccentric medium spiny neuron	0.2 nTPM
Amygdala	0.3 nTPM
Cerebral cortex	0.3 nTPM
Basal ganglia	0.2 nTPM
Hypothalamus	0.2 nTPM
Thalamus	0.1 nTPM
Hippocampus	0.0 nTPM

Endothelial cell	159.1 nTPM
Basal ganglia	220.9 nTPM
Hippocampus	189.1 nTPM
Cerebral cortex	173.9 nTPM
Midbrain	162.6 nTPM
Thalamus	161.0 nTPM
Spinal cord	158.8 nTPM
Pons	155.4 nTPM
Hypothalamus	155.1 nTPM
Amygdala	148.7 nTPM
Cerebellum	135.5 nTPM
Medulla oblongata	89.2 nTPM

Ependymal cell	0.6 nTPM
Spinal cord	1.9 nTPM
Hippocampus	1.2 nTPM
Thalamus	1.2 nTPM
Amygdala	0.6 nTPM
Pons	0.4 nTPM
Basal ganglia	0.2 nTPM
Medulla oblongata	0.2 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM