Single cell type - PCCB - The Human Protein Atlas

PCCB

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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.	PCCB
Gene descriptionⁱ Full gene name according to HGNC.	Propionyl-CoA carboxylase subunit beta
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Enzymes Human disease related genes Metabolic proteins Plasma proteins Potential drug targets
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.	14

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.	Early spermatids - Spermatogenesis (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 (Oocytes, Early spermatids, Late spermatids)
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.	0.48
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 (Oocytes, Early spermatids, Late spermatids)

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

PCCB is part of cluster 21 Early spermatids - Spermatogenesis with confidenceⁱ 1
337 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.
PIWIL3	Piwi like RNA-mediated gene silencing 3	0.6597	21
MYOCOS	Myocilin opposite strand	0.6410	44
CWC15	CWC15 spliceosome associated protein homolog	0.6390	21
MMAA	Metabolism of cobalamin associated A	0.5940	21
ACOT13	Acyl-CoA thioesterase 13	0.5928	56
COQ6	Coenzyme Q6, monooxygenase	0.5844	21
CHRNB4	Cholinergic receptor nicotinic beta 4 subunit	0.5298	11
PCMT1	Protein-L-isoaspartate (D-aspartate) O-methyltransferase	0.5294	21
FDXACB1	Ferredoxin-fold anticodon binding domain containing 1	0.5275	21
NT5DC4	5'-nucleotidase domain containing 4	0.5251	21
LMO1	LIM domain only 1	0.5224	21
TMEM150A	Transmembrane protein 150A	0.5192	24
FAHD1	Fumarylacetoacetate hydrolase domain containing 1	0.5162	56
MALSU1	Mitochondrial assembly of ribosomal large subunit 1	0.5071	39
MAIP1	Matrix AAA peptidase interacting protein 1	0.5063	15

IMMUNE CELLS

PCCB is part of cluster 13 Non-specific - Mitochondria with confidenceⁱ 0.95
458 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.
NDUFS4	NADH:ubiquinone oxidoreductase subunit S4	1.0000	13
SKIC8	SKI8 subunit of superkiller complex	1.0000	13
ITPA	Inosine triphosphatase	0.9762	13
ALG3	ALG3 alpha-1,3- mannosyltransferase	0.9762	13
ATG4B	Autophagy related 4B cysteine peptidase	0.9762	13
PIGF	Phosphatidylinositol glycan anchor biosynthesis class F	0.9762	13
SUMF2	Sulfatase modifying factor 2	0.9762	13
SRSF7	Serine and arginine rich splicing factor 7	0.9762	13
ACOX3	Acyl-CoA oxidase 3, pristanoyl	0.9762	13
TMTC4	Transmembrane O-mannosyltransferase targeting cadherins 4	0.9524	13
RPL26L1	Ribosomal protein L26 like 1	0.9524	13
SEM1	SEM1 26S proteasome subunit	0.9524	13
NDRG1	N-myc downstream regulated 1	0.9524	13
NUTF2	Nuclear transport factor 2	0.9524	13
DUS3L	Dihydrouridine synthase 3 like	0.9524	13

Adipocytes	5.2 nTPM
Breast	5.9 nTPM
Adipose tissue	4.5 nTPM

Alveolar cells type 1	14.5 nTPM
Lung	14.5 nTPM

Alveolar cells type 2	26.6 nTPM
Lung	26.6 nTPM

Astrocytes	15.2 nTPM
Brain	15.2 nTPM

B-cells	8.2 nTPM
Liver	14.5 nTPM
Lung	13.4 nTPM
Thymus	12.8 nTPM
Salivary gland	11.5 nTPM
Bone marrow	9.5 nTPM
Spleen	9.4 nTPM
Stomach	7.6 nTPM
Lymph node	6.6 nTPM
Esophagus	5.9 nTPM
Adipose tissue	5.8 nTPM
Skin	5.1 nTPM
PBMC	4.6 nTPM
Kidney	0.0 nTPM

Ciliated cells	14.7 nTPM
Bronchus	22.6 nTPM
Endometrium	15.3 nTPM
Lung	12.8 nTPM
Fallopian tube	8.3 nTPM

Club cells	21.8 nTPM
Bronchus	39.6 nTPM
Lung	15.9 nTPM
Prostate	10.0 nTPM

Endothelial cells	7.7 nTPM
Placenta	22.1 nTPM
Pancreas	12.9 nTPM
Endometrium	11.4 nTPM
Heart muscle	11.0 nTPM
Tongue	8.8 nTPM
Liver	7.6 nTPM
Lung	7.5 nTPM
Testis	7.3 nTPM
Ovary	7.1 nTPM
Breast	7.0 nTPM
Thymus	6.8 nTPM
Salivary gland	5.3 nTPM
Vascular	4.9 nTPM
Fallopian tube	4.7 nTPM
Skin	4.3 nTPM
Skeletal muscle	4.2 nTPM
Prostate	3.4 nTPM
Esophagus	2.6 nTPM

Enteroendocrine cells	19.9 nTPM
Colon	37.7 nTPM
Rectum	11.7 nTPM
Small intestine	10.3 nTPM

Fibroblasts	11.7 nTPM
Heart muscle	29.2 nTPM
Pancreas	23.1 nTPM
Placenta	13.7 nTPM
Esophagus	12.8 nTPM
Thymus	12.3 nTPM
Salivary gland	11.0 nTPM
Skeletal muscle	10.5 nTPM
Vascular	10.1 nTPM
Adipose tissue	10.0 nTPM
Fallopian tube	9.8 nTPM
Lung	9.6 nTPM
Stomach	8.6 nTPM
Skin	8.3 nTPM
Breast	7.4 nTPM
Liver	7.1 nTPM
Prostate	4.0 nTPM

Granulocytes	8.3 nTPM
Tongue	9.7 nTPM
Lung	8.1 nTPM
Fallopian tube	7.1 nTPM

Intestinal goblet cells	16.9 nTPM
Colon	25.8 nTPM
Small intestine	12.7 nTPM
Rectum	12.1 nTPM

Lymphatic endothelial cells	11.9 nTPM
Ovary	16.4 nTPM
Fallopian tube	7.4 nTPM

Macrophages	11.6 nTPM
Kidney	20.4 nTPM
Pancreas	18.5 nTPM
Lung	18.4 nTPM
Testis	14.9 nTPM
Endometrium	14.1 nTPM
Prostate	13.7 nTPM
Thymus	11.1 nTPM
Tongue	10.8 nTPM
Vascular	10.7 nTPM
Skeletal muscle	10.4 nTPM
Stomach	10.3 nTPM
Bone marrow	10.1 nTPM
Breast	9.7 nTPM
Salivary gland	9.6 nTPM
Fallopian tube	9.2 nTPM
Esophagus	9.0 nTPM
Adipose tissue	8.4 nTPM
Skin	7.8 nTPM
Spleen	4.0 nTPM

Paneth cells	16.9 nTPM
Small intestine	24.2 nTPM
Rectum	15.5 nTPM
Colon	10.9 nTPM

Basal prostatic cells	13.8 nTPM
Prostate	13.8 nTPM

Basal respiratory cells	37.9 nTPM
Bronchus	37.9 nTPM

Basal squamous epithelial cells	6.4 nTPM
Esophagus	6.4 nTPM

Bipolar cells	14.3 nTPM
Eye	14.3 nTPM

Plasma cells	23.5 nTPM
Stomach	35.6 nTPM
Thymus	29.2 nTPM
Liver	26.5 nTPM
Esophagus	26.0 nTPM
Spleen	24.1 nTPM
Salivary gland	17.0 nTPM
Bone marrow	15.1 nTPM
Fallopian tube	14.5 nTPM

Schwann cells	22.0 nTPM
Esophagus	47.9 nTPM
Adipose tissue	11.3 nTPM
Vascular	6.8 nTPM

Serous glandular cells	21.1 nTPM
Salivary gland	24.5 nTPM
Tongue	17.7 nTPM

Smooth muscle cells	10.2 nTPM
Placenta	16.3 nTPM
Endometrium	13.1 nTPM
Tongue	12.6 nTPM
Fallopian tube	12.6 nTPM
Lung	11.8 nTPM
Salivary gland	11.7 nTPM
Thymus	11.0 nTPM
Ovary	10.3 nTPM
Adipose tissue	10.2 nTPM
Breast	8.5 nTPM
Vascular	8.3 nTPM
Skin	7.8 nTPM
Liver	7.6 nTPM
Esophagus	7.2 nTPM
Skeletal muscle	7.1 nTPM
Prostate	6.7 nTPM

Suprabasal keratinocytes	15.8 nTPM
Tongue	27.3 nTPM
Skin	4.3 nTPM

T-cells	9.1 nTPM
Liver	15.6 nTPM
Colon	13.6 nTPM
Kidney	12.4 nTPM
Stomach	12.0 nTPM
Lung	11.4 nTPM
Adipose tissue	10.4 nTPM
Tongue	10.4 nTPM
Endometrium	9.8 nTPM
Fallopian tube	9.4 nTPM
Spleen	9.2 nTPM
Salivary gland	9.2 nTPM
Bone marrow	8.9 nTPM
Thymus	8.9 nTPM
Skin	8.8 nTPM
Lymph node	8.8 nTPM
Prostate	8.4 nTPM
Skeletal muscle	6.4 nTPM
Breast	6.0 nTPM
PBMC	5.1 nTPM
Esophagus	4.9 nTPM
Vascular	2.4 nTPM

Undifferentiated cells	27.2 nTPM
Colon	35.5 nTPM
Small intestine	28.0 nTPM
Rectum	18.2 nTPM

Amygdala excitatory	41.9 nTPM
Thalamus	50.4 nTPM
Hypothalamus	49.3 nTPM
Amygdala	40.1 nTPM
Basal ganglia	38.2 nTPM
Hippocampus	37.3 nTPM
Cerebral cortex	35.9 nTPM

Astrocyte	42.5 nTPM
Amygdala	52.9 nTPM
Hypothalamus	50.6 nTPM
Cerebral cortex	48.3 nTPM
Basal ganglia	44.2 nTPM
Thalamus	43.9 nTPM
Midbrain	42.8 nTPM
Hippocampus	40.9 nTPM
Cerebellum	40.4 nTPM
Pons	36.0 nTPM
Medulla oblongata	34.0 nTPM
Spinal cord	33.9 nTPM

Bergmann glia	53.2 nTPM
Pons	57.5 nTPM
Medulla oblongata	51.1 nTPM
Cerebellum	51.0 nTPM

Central nervous system macrophage	38.9 nTPM
Hypothalamus	46.4 nTPM
Amygdala	45.6 nTPM
Midbrain	42.4 nTPM
Thalamus	40.4 nTPM
Cerebellum	39.0 nTPM
Basal ganglia	36.6 nTPM
Pons	36.6 nTPM
Hippocampus	35.7 nTPM
Medulla oblongata	35.5 nTPM
Spinal cord	35.3 nTPM
Cerebral cortex	34.8 nTPM

Cerebellar inhibitory	45.1 nTPM
Spinal cord	55.0 nTPM
Cerebellum	45.8 nTPM
Midbrain	43.2 nTPM
Medulla oblongata	41.1 nTPM
Pons	40.3 nTPM

Cge interneuron	55.4 nTPM
Hypothalamus	68.1 nTPM
Amygdala	58.8 nTPM
Cerebral cortex	52.9 nTPM
Thalamus	52.3 nTPM
Hippocampus	52.2 nTPM
Midbrain	52.1 nTPM
Basal ganglia	51.0 nTPM

Choroid plexus epithelial cell	53.2 nTPM
Basal ganglia	62.3 nTPM
Thalamus	54.8 nTPM
Medulla oblongata	51.5 nTPM
Hippocampus	44.4 nTPM

Committed oligodendrocyte precursor	74.2 nTPM
Hypothalamus	111.3 nTPM
Amygdala	95.9 nTPM
Cerebral cortex	85.5 nTPM
Hippocampus	81.2 nTPM
Thalamus	76.5 nTPM
Spinal cord	69.9 nTPM
Basal ganglia	67.9 nTPM
Midbrain	67.2 nTPM
Cerebellum	63.4 nTPM
Medulla oblongata	51.6 nTPM
Pons	46.0 nTPM

Deep-layer corticothalamic and 6b	35.1 nTPM
Hypothalamus	49.4 nTPM
Amygdala	40.2 nTPM
Cerebral cortex	34.9 nTPM
Basal ganglia	33.2 nTPM
Hippocampus	32.6 nTPM
Midbrain	20.0 nTPM

Deep-layer intratelencephalic	41.1 nTPM
Hypothalamus	48.4 nTPM
Amygdala	43.3 nTPM
Hippocampus	40.8 nTPM
Cerebral cortex	37.7 nTPM
Basal ganglia	35.4 nTPM

Deep-layer near-projecting	34.8 nTPM
Hypothalamus	45.6 nTPM
Amygdala	36.6 nTPM
Cerebral cortex	32.0 nTPM
Basal ganglia	31.4 nTPM
Hippocampus	28.6 nTPM

Eccentric medium spiny neuron	36.6 nTPM
Thalamus	39.7 nTPM
Amygdala	37.2 nTPM
Hypothalamus	37.2 nTPM
Hippocampus	36.1 nTPM
Cerebral cortex	35.8 nTPM
Basal ganglia	33.6 nTPM

Endothelial cell	24.7 nTPM
Thalamus	36.1 nTPM
Midbrain	31.2 nTPM
Hypothalamus	29.8 nTPM
Medulla oblongata	27.7 nTPM
Cerebral cortex	24.9 nTPM
Basal ganglia	24.2 nTPM
Spinal cord	24.2 nTPM
Hippocampus	21.5 nTPM
Cerebellum	18.6 nTPM
Amygdala	17.9 nTPM
Pons	15.6 nTPM