Single cell type - SP140 - The Human Protein Atlas

SP140

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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.	SP140
Gene descriptionⁱ Full gene name according to HGNC.	SP140 nuclear body protein
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Transcription factors
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.	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.	B-cells - B-cell 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 (B-cells, Plasma cells, NK-cells, T-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.	0.82
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.	Group enriched (Central nervous system macrophage, Leukocyte)
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 (memory B-cell)
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 (B-cells, Plasma cells, NK-cells, T-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: Group enriched (Central nervous system macrophage, Leukocyte)

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 (memory B-cell)
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

SP140 is part of cluster 73 B-cells - B-cell function with confidenceⁱ 1
195 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.
CD19	CD19 molecule	0.9185	73
MS4A1	Membrane spanning 4-domains A1	0.9099	73
FCRL1	Fc receptor like 1	0.9087	73
PAX5	Paired box 5	0.9041	73
LY9	Lymphocyte antigen 9	0.9041	73
BANK1	B cell scaffold protein with ankyrin repeats 1	0.9017	73
CXCR5	C-X-C motif chemokine receptor 5	0.8973	73
FCRLA	Fc receptor like A	0.8954	73
FCRL2	Fc receptor like 2	0.8865	73
VPREB3	V-set pre-B cell surrogate light chain 3	0.8835	73
BLK	BLK proto-oncogene, Src family tyrosine kinase	0.8828	73
FCER2	Fc epsilon receptor II	0.8766	73
ZNF860	Zinc finger protein 860	0.8702	73
PARP15	Poly(ADP-ribose) polymerase family member 15	0.8700	73
AIM2	Absent in melanoma 2	0.8622	73

IMMUNE CELLS

SP140 is part of cluster 24 Non-specific - Transcription with confidenceⁱ 0.96
516 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.
ZNF85	Zinc finger protein 85	0.9524	24
FAM117B	Family with sequence similarity 117 member B	0.9524	24
ZNF813	Zinc finger protein 813	0.9286	24
SMAGP	Small cell adhesion glycoprotein	0.9286	24
ANAPC1	Anaphase promoting complex subunit 1	0.9286	24
ZNF225	Zinc finger protein 225	0.9048	3
ZNF786	Zinc finger protein 786	0.9048	24
ZNF799	Zinc finger protein 799	0.9048	24
ZNF383	Zinc finger protein 383	0.9048	24
ATF7IP	Activating transcription factor 7 interacting protein	0.9048	14
FHIP2B	FHF complex subunit HOOK interacting protein 2B	0.9048	24
TTPAL	Alpha tocopherol transfer protein like	0.9048	24
AFF4	ALF transcription elongation factor 4	0.9048	24
IFT88	Intraflagellar transport 88	0.9048	14
SPRYD7	SPRY domain containing 7	0.8810	14

Adipocytes	1.3 nTPM
Breast	1.4 nTPM
Adipose tissue	1.2 nTPM

Alveolar cells type 1	0.1 nTPM
Lung	0.1 nTPM

Alveolar cells type 2	0.2 nTPM
Lung	0.2 nTPM

Astrocytes	3.7 nTPM
Brain	3.7 nTPM

B-cells	146.0 nTPM
Lymph node	242.8 nTPM
Bone marrow	216.6 nTPM
Stomach	210.5 nTPM
Spleen	166.0 nTPM
Thymus	154.9 nTPM
Salivary gland	147.7 nTPM
Esophagus	147.5 nTPM
Adipose tissue	146.9 nTPM
PBMC	143.2 nTPM
Lung	138.2 nTPM
Liver	86.9 nTPM
Kidney	72.8 nTPM
Skin	23.7 nTPM

Ciliated cells	1.3 nTPM
Lung	1.8 nTPM
Bronchus	1.6 nTPM
Fallopian tube	1.1 nTPM
Endometrium	0.5 nTPM

Club cells	0.8 nTPM
Lung	1.8 nTPM
Bronchus	0.4 nTPM
Prostate	0.3 nTPM

Endothelial cells	0.9 nTPM
Liver	3.8 nTPM
Thymus	3.0 nTPM
Heart muscle	1.9 nTPM
Esophagus	1.8 nTPM
Salivary gland	1.0 nTPM
Skin	0.9 nTPM
Lung	0.8 nTPM
Skeletal muscle	0.7 nTPM
Placenta	0.6 nTPM
Prostate	0.5 nTPM
Testis	0.3 nTPM
Tongue	0.3 nTPM
Vascular	0.3 nTPM
Fallopian tube	0.2 nTPM
Endometrium	0.1 nTPM
Ovary	0.1 nTPM
Pancreas	0.0 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	0.1 nTPM
Colon	0.3 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	1.0 nTPM
Stomach	2.9 nTPM
Salivary gland	2.6 nTPM
Thymus	2.5 nTPM
Lung	1.5 nTPM
Liver	1.2 nTPM
Pancreas	1.2 nTPM
Esophagus	0.9 nTPM
Breast	0.9 nTPM
Prostate	0.7 nTPM
Skin	0.6 nTPM
Heart muscle	0.5 nTPM
Vascular	0.3 nTPM
Fallopian tube	0.3 nTPM
Skeletal muscle	0.1 nTPM
Adipose tissue	0.1 nTPM
Placenta	0.0 nTPM

Granulocytes	0.2 nTPM
Fallopian tube	0.6 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

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

Lymphatic endothelial cells	0.4 nTPM
Fallopian tube	0.7 nTPM
Ovary	0.0 nTPM

Macrophages	13.2 nTPM
Lung	39.4 nTPM
Kidney	20.4 nTPM
Bone marrow	18.2 nTPM
Fallopian tube	18.0 nTPM
Adipose tissue	15.4 nTPM
Breast	14.2 nTPM
Salivary gland	13.7 nTPM
Skeletal muscle	13.5 nTPM
Stomach	12.9 nTPM
Tongue	12.9 nTPM
Prostate	12.1 nTPM
Endometrium	11.7 nTPM
Thymus	10.7 nTPM
Spleen	9.0 nTPM
Testis	7.4 nTPM
Skin	6.7 nTPM
Esophagus	6.4 nTPM
Vascular	5.7 nTPM
Pancreas	2.1 nTPM

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

Cone photoreceptor cells	1.7 nTPM
Eye	1.7 nTPM

Early spermatids	24.2 nTPM
Testis	24.2 nTPM

Plasma cells	74.9 nTPM
Bone marrow	119.3 nTPM
Thymus	109.8 nTPM
Spleen	103.4 nTPM
Stomach	64.9 nTPM
Liver	61.1 nTPM
Salivary gland	54.6 nTPM
Esophagus	46.8 nTPM
Fallopian tube	39.2 nTPM

Schwann cells	14.4 nTPM
Adipose tissue	43.3 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	1.5 nTPM
Salivary gland	3.0 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	1.1 nTPM
Thymus	4.6 nTPM
Esophagus	3.6 nTPM
Lung	2.4 nTPM
Salivary gland	1.4 nTPM
Breast	1.3 nTPM
Tongue	0.9 nTPM
Liver	0.8 nTPM
Placenta	0.7 nTPM
Prostate	0.6 nTPM
Skin	0.3 nTPM
Skeletal muscle	0.2 nTPM
Vascular	0.2 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.1 nTPM
Endometrium	0.0 nTPM
Adipose tissue	0.0 nTPM

T-cells	58.3 nTPM
Adipose tissue	104.5 nTPM
Colon	84.8 nTPM
Fallopian tube	83.3 nTPM
Bone marrow	82.6 nTPM
Esophagus	70.6 nTPM
Stomach	68.0 nTPM
Spleen	67.6 nTPM
Lung	66.1 nTPM
Tongue	62.3 nTPM
Skeletal muscle	57.8 nTPM
Prostate	51.9 nTPM
Lymph node	50.2 nTPM
Kidney	47.9 nTPM
Vascular	47.4 nTPM
Skin	45.2 nTPM
Breast	43.9 nTPM
Thymus	43.5 nTPM
Liver	41.3 nTPM
PBMC	37.7 nTPM
Salivary gland	34.8 nTPM
Endometrium	32.4 nTPM

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

Amygdala excitatory	7.0 nTPM
Hypothalamus	8.8 nTPM
Basal ganglia	8.2 nTPM
Amygdala	7.3 nTPM
Cerebral cortex	7.0 nTPM
Hippocampus	6.5 nTPM
Thalamus	4.5 nTPM

Astrocyte	10.7 nTPM
Hypothalamus	18.7 nTPM
Amygdala	12.5 nTPM
Midbrain	10.7 nTPM
Basal ganglia	10.6 nTPM
Pons	10.6 nTPM
Spinal cord	10.5 nTPM
Hippocampus	9.2 nTPM
Cerebral cortex	9.1 nTPM
Thalamus	8.9 nTPM
Medulla oblongata	8.8 nTPM
Cerebellum	8.6 nTPM

Bergmann glia	3.2 nTPM
Cerebellum	6.2 nTPM
Medulla oblongata	2.1 nTPM
Pons	1.4 nTPM

Central nervous system macrophage	141.9 nTPM
Amygdala	221.6 nTPM
Hypothalamus	196.4 nTPM
Hippocampus	145.4 nTPM
Thalamus	143.6 nTPM
Midbrain	135.3 nTPM
Cerebral cortex	126.9 nTPM
Cerebellum	125.6 nTPM
Basal ganglia	125.0 nTPM
Pons	124.2 nTPM
Medulla oblongata	110.4 nTPM
Spinal cord	106.0 nTPM

Cerebellar inhibitory	6.0 nTPM
Midbrain	7.2 nTPM
Cerebellum	6.1 nTPM
Medulla oblongata	5.9 nTPM
Spinal cord	5.5 nTPM
Pons	5.3 nTPM

Cge interneuron	7.0 nTPM
Hypothalamus	7.7 nTPM
Amygdala	7.6 nTPM
Thalamus	7.6 nTPM
Basal ganglia	7.1 nTPM
Midbrain	7.0 nTPM
Cerebral cortex	6.5 nTPM
Hippocampus	5.8 nTPM

Choroid plexus epithelial cell	1.4 nTPM
Thalamus	2.7 nTPM
Medulla oblongata	1.5 nTPM
Basal ganglia	1.2 nTPM
Hippocampus	0.0 nTPM

Committed oligodendrocyte precursor	2.6 nTPM
Hippocampus	5.2 nTPM
Thalamus	4.3 nTPM
Amygdala	3.4 nTPM
Midbrain	3.4 nTPM
Basal ganglia	3.3 nTPM
Hypothalamus	2.7 nTPM
Pons	2.7 nTPM
Cerebellum	1.6 nTPM
Cerebral cortex	1.3 nTPM
Medulla oblongata	1.3 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	7.9 nTPM
Hypothalamus	10.5 nTPM
Amygdala	9.3 nTPM
Cerebral cortex	8.3 nTPM
Basal ganglia	8.1 nTPM
Hippocampus	6.8 nTPM
Midbrain	4.4 nTPM

Deep-layer intratelencephalic	7.2 nTPM
Hypothalamus	9.8 nTPM
Hippocampus	6.9 nTPM
Basal ganglia	6.6 nTPM
Cerebral cortex	6.6 nTPM
Amygdala	6.1 nTPM

Deep-layer near-projecting	8.2 nTPM
Hypothalamus	10.7 nTPM
Amygdala	8.6 nTPM
Basal ganglia	8.3 nTPM
Hippocampus	7.5 nTPM
Cerebral cortex	6.2 nTPM

Eccentric medium spiny neuron	6.5 nTPM
Cerebral cortex	7.4 nTPM
Amygdala	7.2 nTPM
Thalamus	6.6 nTPM
Basal ganglia	6.4 nTPM
Hypothalamus	6.2 nTPM
Hippocampus	5.0 nTPM

Endothelial cell	16.7 nTPM
Midbrain	25.5 nTPM
Cerebellum	23.2 nTPM
Pons	23.1 nTPM
Hypothalamus	22.3 nTPM
Basal ganglia	20.5 nTPM
Thalamus	19.2 nTPM
Hippocampus	14.4 nTPM
Cerebral cortex	12.1 nTPM
Spinal cord	12.1 nTPM
Medulla oblongata	7.2 nTPM
Amygdala	4.5 nTPM

Ependymal cell	19.9 nTPM
Amygdala	30.1 nTPM
Hippocampus	28.4 nTPM
Basal ganglia	23.7 nTPM
Spinal cord	23.0 nTPM
Hypothalamus	21.4 nTPM
Midbrain	14.6 nTPM
Medulla oblongata	14.3 nTPM
Thalamus	13.0 nTPM
Pons	10.6 nTPM