Single cell type - SMC4 - The Human Protein Atlas

SMC4

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Pathway

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.	SMC4
Gene descriptionⁱ Full gene name according to HGNC.	Structural maintenance of chromosomes 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma proteins
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.	12

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.	Non-specific - Cell proliferation (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 (Spermatocytes, Erythroid cells, Spermatogonia)
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.	0.43
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 (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 (basophil)
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 (Spermatocytes, Erythroid cells, Spermatogonia)

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 (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 (basophil)
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

SMC4 is part of cluster 52 Non-specific - Cell proliferation with confidenceⁱ 1
248 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.
CDCA8	Cell division cycle associated 8	0.8258	52
CKAP2L	Cytoskeleton associated protein 2 like	0.8175	52
HMGB2	High mobility group box 2	0.7861	52
GTSE1	G2 and S-phase expressed 1	0.7821	52
CENPE	Centromere protein E	0.7796	52
KIF20B	Kinesin family member 20B	0.7703	52
NUSAP1	Nucleolar and spindle associated protein 1	0.7638	52
TOP2A	DNA topoisomerase II alpha	0.7423	52
NCAPG	Non-SMC condensin I complex subunit G	0.7410	52
SMC2	Structural maintenance of chromosomes 2	0.7361	52
FANCI	FA complementation group I	0.7353	52
PRR11	Proline rich 11	0.7312	52
SKA1	Spindle and kinetochore associated complex subunit 1	0.7308	52
CDK1	Cyclin dependent kinase 1	0.7305	52
SPC24	SPC24 component of NDC80 kinetochore complex	0.7277	52

IMMUNE CELLS

SMC4 is part of cluster 42 Non-specific - Vesicular transport with confidenceⁱ 1
519 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.
SPECC1L	Sperm antigen with calponin homology and coiled-coil domains 1 like	1.0000	42
METTL14	Methyltransferase 14, N6-adenosine-methyltransferase subunit	1.0000	42
FBXO28	F-box protein 28	1.0000	42
ZC3H7A	Zinc finger CCCH-type containing 7A	1.0000	42
TES	Testin LIM domain protein	1.0000	42
RNF168	Ring finger protein 168	0.9762	42
AP5M1	Adaptor related protein complex 5 subunit mu 1	0.9762	42
TOPBP1	DNA topoisomerase II binding protein 1	0.9762	42
CCDC82	Coiled-coil domain containing 82	0.9762	42
MINDY3	MINDY lysine 48 deubiquitinase 3	0.9762	42
RNASEL	Ribonuclease L	0.9762	42
IMPA1	Inositol monophosphatase 1	0.9762	42
BLZF1	Basic leucine zipper nuclear factor 1	0.9762	42
SMAP1	Small ArfGAP 1	0.9762	42
PARP4	Poly(ADP-ribose) polymerase family member 4	0.9762	42

Adipocytes	23.2 nTPM
Breast	25.9 nTPM
Adipose tissue	20.6 nTPM

Alveolar cells type 1	20.9 nTPM
Lung	20.9 nTPM

Alveolar cells type 2	64.9 nTPM
Lung	64.9 nTPM

Astrocytes	3.7 nTPM
Brain	3.7 nTPM

B-cells	28.0 nTPM
Skin	55.9 nTPM
Salivary gland	44.1 nTPM
Lung	36.2 nTPM
PBMC	33.9 nTPM
Adipose tissue	33.7 nTPM
Liver	29.0 nTPM
Lymph node	26.8 nTPM
Stomach	21.9 nTPM
Spleen	18.3 nTPM
Esophagus	17.7 nTPM
Thymus	17.0 nTPM
Kidney	15.6 nTPM
Bone marrow	14.3 nTPM

Ciliated cells	22.9 nTPM
Endometrium	35.7 nTPM
Lung	20.3 nTPM
Fallopian tube	19.6 nTPM
Bronchus	16.1 nTPM

Club cells	18.9 nTPM
Lung	22.7 nTPM
Bronchus	19.8 nTPM
Prostate	14.3 nTPM

Dendritic cells	59.7 nTPM
Adipose tissue	69.0 nTPM
PBMC	50.4 nTPM

Endothelial cells	38.9 nTPM
Heart muscle	64.2 nTPM
Placenta	63.6 nTPM
Testis	58.0 nTPM
Ovary	56.7 nTPM
Endometrium	53.0 nTPM
Liver	50.4 nTPM
Vascular	39.4 nTPM
Skeletal muscle	37.8 nTPM
Pancreas	36.2 nTPM
Prostate	34.7 nTPM
Breast	34.3 nTPM
Fallopian tube	30.8 nTPM
Tongue	30.3 nTPM
Lung	26.3 nTPM
Salivary gland	25.8 nTPM
Thymus	21.5 nTPM
Skin	20.8 nTPM
Esophagus	16.8 nTPM

Enteroendocrine cells	36.4 nTPM
Colon	45.0 nTPM
Rectum	36.9 nTPM
Small intestine	27.5 nTPM

Erythroid cells	267.9 nTPM
Liver	405.6 nTPM
Bone marrow	130.2 nTPM

Fibroblasts	32.6 nTPM
Pancreas	121.7 nTPM
Heart muscle	96.8 nTPM
Liver	48.6 nTPM
Placenta	47.1 nTPM
Vascular	37.6 nTPM
Fallopian tube	21.4 nTPM
Skeletal muscle	21.2 nTPM
Skin	18.4 nTPM
Esophagus	18.1 nTPM
Prostate	17.2 nTPM
Salivary gland	15.2 nTPM
Breast	14.7 nTPM
Stomach	13.0 nTPM
Adipose tissue	11.1 nTPM
Lung	9.9 nTPM
Thymus	9.4 nTPM

Granulocytes	49.9 nTPM
Tongue	72.8 nTPM
Lung	39.8 nTPM
Fallopian tube	37.1 nTPM

Intestinal goblet cells	39.1 nTPM
Colon	58.1 nTPM
Small intestine	36.6 nTPM
Rectum	22.6 nTPM

Lymphatic endothelial cells	44.6 nTPM
Fallopian tube	56.5 nTPM
Ovary	32.7 nTPM

Basal keratinocytes	49.8 nTPM
Tongue	56.2 nTPM
Skin	43.4 nTPM

Basal prostatic cells	33.1 nTPM
Prostate	33.1 nTPM

Basal respiratory cells	33.1 nTPM
Bronchus	33.1 nTPM

Basal squamous epithelial cells	31.5 nTPM
Esophagus	31.5 nTPM

Macrophages	33.6 nTPM
Tongue	60.1 nTPM
Testis	53.9 nTPM
Esophagus	51.4 nTPM
Endometrium	48.0 nTPM
Fallopian tube	47.2 nTPM
Adipose tissue	43.5 nTPM
Skeletal muscle	34.0 nTPM
Pancreas	32.9 nTPM
Prostate	32.5 nTPM
Breast	31.9 nTPM
Vascular	30.1 nTPM
Skin	27.9 nTPM
Salivary gland	25.9 nTPM
Lung	25.6 nTPM
Bone marrow	24.3 nTPM
Spleen	22.1 nTPM
Thymus	18.7 nTPM
Kidney	18.6 nTPM
Stomach	10.3 nTPM

Paneth cells	23.2 nTPM
Rectum	34.2 nTPM
Colon	18.1 nTPM
Small intestine	17.3 nTPM

Plasma cells	105.8 nTPM
Liver	217.3 nTPM
Spleen	181.4 nTPM
Thymus	167.4 nTPM
Bone marrow	145.0 nTPM
Salivary gland	56.0 nTPM
Stomach	51.9 nTPM
Fallopian tube	17.4 nTPM
Esophagus	10.4 nTPM

Schwann cells	19.9 nTPM
Adipose tissue	41.4 nTPM
Vascular	18.3 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	19.0 nTPM
Tongue	26.5 nTPM
Salivary gland	11.5 nTPM

Smooth muscle cells	31.2 nTPM
Endometrium	81.2 nTPM
Placenta	67.7 nTPM
Vascular	49.7 nTPM
Skeletal muscle	40.9 nTPM
Ovary	40.3 nTPM
Liver	31.4 nTPM
Skin	24.9 nTPM
Adipose tissue	24.9 nTPM
Prostate	24.3 nTPM
Esophagus	24.0 nTPM
Breast	23.1 nTPM
Tongue	20.4 nTPM
Fallopian tube	16.7 nTPM
Lung	10.6 nTPM
Thymus	10.5 nTPM
Salivary gland	9.0 nTPM

Suprabasal keratinocytes	36.3 nTPM
Skin	40.3 nTPM
Tongue	32.3 nTPM

T-cells	54.8 nTPM
Colon	144.3 nTPM
Tongue	105.9 nTPM
Endometrium	77.1 nTPM
Adipose tissue	71.6 nTPM
Liver	69.0 nTPM
Skin	68.0 nTPM
Skeletal muscle	63.5 nTPM
Kidney	53.2 nTPM
Esophagus	51.1 nTPM
Breast	50.2 nTPM
Fallopian tube	48.9 nTPM
Salivary gland	45.6 nTPM
PBMC	43.9 nTPM
Vascular	39.8 nTPM
Spleen	37.0 nTPM
Lymph node	36.5 nTPM
Lung	36.3 nTPM
Stomach	31.0 nTPM
Thymus	26.5 nTPM
Bone marrow	26.2 nTPM
Prostate	25.4 nTPM

Undifferentiated cells	108.4 nTPM
Colon	149.7 nTPM
Rectum	88.6 nTPM
Small intestine	86.9 nTPM

Amygdala excitatory	5.9 nTPM
Thalamus	8.2 nTPM
Hypothalamus	6.7 nTPM
Amygdala	6.3 nTPM
Hippocampus	5.2 nTPM
Cerebral cortex	5.1 nTPM
Basal ganglia	3.7 nTPM

Astrocyte	11.8 nTPM
Amygdala	19.1 nTPM
Hypothalamus	13.7 nTPM
Basal ganglia	13.3 nTPM
Cerebral cortex	12.1 nTPM
Pons	11.5 nTPM
Cerebellum	11.2 nTPM
Hippocampus	10.8 nTPM
Midbrain	10.5 nTPM
Thalamus	9.6 nTPM
Medulla oblongata	8.9 nTPM
Spinal cord	8.4 nTPM

Bergmann glia	22.9 nTPM
Pons	30.2 nTPM
Cerebellum	23.6 nTPM
Medulla oblongata	14.9 nTPM

Central nervous system macrophage	39.0 nTPM
Spinal cord	47.7 nTPM
Amygdala	46.7 nTPM
Hypothalamus	42.8 nTPM
Basal ganglia	41.2 nTPM
Midbrain	39.8 nTPM
Hippocampus	38.2 nTPM
Cerebellum	37.4 nTPM
Cerebral cortex	37.1 nTPM
Pons	33.3 nTPM
Thalamus	33.1 nTPM
Medulla oblongata	32.1 nTPM

Cerebellar inhibitory	4.4 nTPM
Midbrain	8.1 nTPM
Cerebellum	6.0 nTPM
Pons	5.0 nTPM
Medulla oblongata	2.8 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	3.9 nTPM
Thalamus	5.5 nTPM
Midbrain	5.0 nTPM
Basal ganglia	3.7 nTPM
Hippocampus	3.6 nTPM
Amygdala	3.4 nTPM
Cerebral cortex	3.3 nTPM
Hypothalamus	2.6 nTPM

Choroid plexus epithelial cell	9.8 nTPM
Hippocampus	11.1 nTPM
Medulla oblongata	10.2 nTPM
Basal ganglia	9.7 nTPM
Thalamus	8.2 nTPM

Committed oligodendrocyte precursor	17.4 nTPM
Amygdala	26.5 nTPM
Thalamus	25.4 nTPM
Basal ganglia	23.5 nTPM
Cerebral cortex	22.8 nTPM
Midbrain	21.0 nTPM
Hippocampus	17.1 nTPM
Hypothalamus	13.7 nTPM
Medulla oblongata	12.9 nTPM
Spinal cord	11.0 nTPM
Pons	10.6 nTPM
Cerebellum	6.3 nTPM

Deep-layer corticothalamic and 6b	4.5 nTPM
Amygdala	5.7 nTPM
Cerebral cortex	5.1 nTPM
Hippocampus	4.6 nTPM
Basal ganglia	4.3 nTPM
Hypothalamus	3.9 nTPM
Midbrain	3.3 nTPM

Deep-layer intratelencephalic	5.4 nTPM
Hippocampus	6.2 nTPM
Amygdala	6.0 nTPM
Basal ganglia	5.9 nTPM
Cerebral cortex	5.3 nTPM
Hypothalamus	3.5 nTPM

Deep-layer near-projecting	1.7 nTPM
Basal ganglia	2.5 nTPM
Cerebral cortex	2.0 nTPM
Amygdala	1.6 nTPM
Hypothalamus	1.3 nTPM
Hippocampus	1.0 nTPM