Single cell type - HDDC2 - The Human Protein Atlas

HDDC2

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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.	HDDC2
Gene descriptionⁱ Full gene name according to HGNC.	HD domain containing 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.	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.	Non-specific - Basic cellular processes (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.	Low cell type specificity
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.	0.28
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: Low cell type specificity

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

HDDC2 is part of cluster 39 Non-specific - Basic cellular processes with confidenceⁱ 0.98
835 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.
TYW3	TRNA-yW synthesizing protein 3 homolog	0.4909	64
PEX7	Peroxisomal biogenesis factor 7	0.4896	17
RWDD1	RWD domain containing 1	0.4885	64
NT5C3B	5'-nucleotidase, cytosolic IIIB	0.4830	31
UQCRH	Ubiquinol-cytochrome c reductase hinge protein	0.4799	39
COA6	Cytochrome c oxidase assembly factor 6	0.4760	58
MRPS23	Mitochondrial ribosomal protein S23	0.4716	39
PTPN20	Protein tyrosine phosphatase non-receptor type 20	0.4713	13
COX14	Cytochrome c oxidase assembly factor COX14	0.4712	39
ABHD10	Abhydrolase domain containing 10, depalmitoylase	0.4694	39
ATP6V0D2	ATPase H+ transporting V0 subunit d2	0.4635	58
EIF2A	Eukaryotic translation initiation factor 2A	0.4613	64
COPS9	COP9 signalosome subunit 9	0.4608	39
BOLA3	BolA family member 3	0.4582	39
EMX2	Empty spiracles homeobox 2	0.4521	3

IMMUNE CELLS

HDDC2 is part of cluster 43 Non-specific - Transcription & Translation with confidenceⁱ 0.99
433 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.
DCUN1D4	Defective in cullin neddylation 1 domain containing 4	1.0000	43
RPL24	Ribosomal protein L24	1.0000	43
RPS4Y1	Ribosomal protein S4 Y-linked 1	1.0000	43
RPS14	Ribosomal protein S14	1.0000	43
CHCHD6	Coiled-coil-helix-coiled-coil-helix domain containing 6	1.0000	43
RPL31	Ribosomal protein L31	0.9762	43
RPS18	Ribosomal protein S18	0.9762	43
RPS4X	Ribosomal protein S4 X-linked	0.9762	43
RPL13	Ribosomal protein L13	0.9762	43
RPL27A	Ribosomal protein L27a	0.9762	43
RPS6	Ribosomal protein S6	0.9762	43
ZNF414	Zinc finger protein 414	0.9762	43
KAT2A	Lysine acetyltransferase 2A	0.9762	43
RPL13A	Ribosomal protein L13a	0.9524	43
RPL11	Ribosomal protein L11	0.9524	43

Adipocytes	21.6 nTPM
Breast	28.7 nTPM
Adipose tissue	14.4 nTPM

Alveolar cells type 1	39.7 nTPM
Lung	39.7 nTPM

Alveolar cells type 2	68.4 nTPM
Lung	68.4 nTPM

Astrocytes	21.4 nTPM
Brain	21.4 nTPM

B-cells	35.6 nTPM
PBMC	61.6 nTPM
Lung	59.0 nTPM
Kidney	57.2 nTPM
Salivary gland	44.9 nTPM
Spleen	35.5 nTPM
Liver	33.8 nTPM
Skin	32.2 nTPM
Bone marrow	31.2 nTPM
Thymus	29.1 nTPM
Lymph node	22.1 nTPM
Adipose tissue	19.3 nTPM
Stomach	18.6 nTPM
Esophagus	17.7 nTPM

Ciliated cells	43.0 nTPM
Endometrium	50.5 nTPM
Fallopian tube	46.2 nTPM
Lung	41.6 nTPM
Bronchus	33.6 nTPM

Club cells	54.3 nTPM
Bronchus	63.7 nTPM
Lung	63.6 nTPM
Prostate	35.5 nTPM

Dendritic cells	25.7 nTPM
PBMC	36.0 nTPM
Adipose tissue	15.4 nTPM

Endothelial cells	21.3 nTPM
Tongue	42.6 nTPM
Breast	37.8 nTPM
Pancreas	31.0 nTPM
Placenta	30.7 nTPM
Heart muscle	30.5 nTPM
Ovary	30.1 nTPM
Testis	25.9 nTPM
Prostate	25.5 nTPM
Lung	23.2 nTPM
Skin	17.4 nTPM
Skeletal muscle	14.5 nTPM
Fallopian tube	13.3 nTPM
Endometrium	12.3 nTPM
Salivary gland	11.9 nTPM
Thymus	10.6 nTPM
Liver	10.1 nTPM
Esophagus	9.1 nTPM
Vascular	7.2 nTPM

Enteroendocrine cells	69.5 nTPM
Small intestine	89.3 nTPM
Colon	77.4 nTPM
Rectum	41.9 nTPM

Fibroblasts	64.5 nTPM
Pancreas	113.3 nTPM
Heart muscle	107.4 nTPM
Placenta	101.6 nTPM
Lung	87.3 nTPM
Breast	77.1 nTPM
Adipose tissue	69.3 nTPM
Thymus	66.6 nTPM
Fallopian tube	64.1 nTPM
Vascular	62.0 nTPM
Prostate	58.1 nTPM
Skeletal muscle	49.9 nTPM
Salivary gland	47.3 nTPM
Esophagus	42.5 nTPM
Stomach	41.8 nTPM
Skin	40.6 nTPM
Liver	3.6 nTPM

Granulocytes	47.3 nTPM
Lung	59.5 nTPM
Fallopian tube	48.6 nTPM
Tongue	34.0 nTPM

Intestinal goblet cells	68.6 nTPM
Colon	86.6 nTPM
Rectum	74.4 nTPM
Small intestine	44.7 nTPM

Lymphatic endothelial cells	19.8 nTPM
Ovary	21.8 nTPM
Fallopian tube	17.8 nTPM

Macrophages	37.7 nTPM
Lung	176.2 nTPM
Kidney	53.1 nTPM
Pancreas	49.3 nTPM
Testis	49.0 nTPM
Prostate	38.6 nTPM
Thymus	35.6 nTPM
Vascular	32.8 nTPM
Bone marrow	30.4 nTPM
Tongue	30.2 nTPM
Breast	30.1 nTPM
Skin	27.9 nTPM
Salivary gland	26.8 nTPM
Spleen	26.1 nTPM
Stomach	25.7 nTPM
Endometrium	23.4 nTPM
Skeletal muscle	18.4 nTPM
Fallopian tube	18.2 nTPM
Adipose tissue	12.7 nTPM
Esophagus	11.6 nTPM

Basal prostatic cells	89.2 nTPM
Prostate	89.2 nTPM

Basal respiratory cells	110.1 nTPM
Bronchus	110.1 nTPM

Basal squamous epithelial cells	64.0 nTPM
Esophagus	64.0 nTPM

Bipolar cells	54.6 nTPM
Eye	54.6 nTPM

Paneth cells	58.4 nTPM
Rectum	65.8 nTPM
Small intestine	58.7 nTPM
Colon	50.7 nTPM

Plasma cells	55.7 nTPM
Liver	72.1 nTPM
Thymus	70.0 nTPM
Bone marrow	66.4 nTPM
Spleen	61.1 nTPM
Fallopian tube	48.2 nTPM
Esophagus	46.8 nTPM
Salivary gland	42.5 nTPM
Stomach	38.1 nTPM

Schwann cells	14.6 nTPM
Vascular	23.0 nTPM
Adipose tissue	20.7 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	107.3 nTPM
Salivary gland	139.4 nTPM
Tongue	75.1 nTPM

Smooth muscle cells	61.9 nTPM
Placenta	108.8 nTPM
Breast	87.8 nTPM
Ovary	80.6 nTPM
Prostate	77.9 nTPM
Skin	74.3 nTPM
Salivary gland	69.8 nTPM
Vascular	68.7 nTPM
Lung	60.0 nTPM
Esophagus	56.5 nTPM
Fallopian tube	54.4 nTPM
Thymus	51.3 nTPM
Tongue	48.2 nTPM
Skeletal muscle	47.5 nTPM
Endometrium	45.9 nTPM
Adipose tissue	45.4 nTPM
Liver	13.2 nTPM

Suprabasal keratinocytes	64.8 nTPM
Tongue	87.5 nTPM
Skin	42.1 nTPM

T-cells	45.5 nTPM
Liver	79.0 nTPM
PBMC	78.7 nTPM
Kidney	76.3 nTPM
Lung	73.2 nTPM
Prostate	66.3 nTPM
Salivary gland	54.8 nTPM
Skeletal muscle	52.6 nTPM
Bone marrow	48.3 nTPM
Breast	43.2 nTPM
Spleen	39.4 nTPM
Thymus	37.0 nTPM
Lymph node	35.1 nTPM
Endometrium	33.9 nTPM
Stomach	33.8 nTPM
Fallopian tube	33.0 nTPM
Tongue	32.9 nTPM
Skin	32.2 nTPM
Colon	31.2 nTPM
Vascular	28.5 nTPM
Adipose tissue	26.3 nTPM
Esophagus	19.5 nTPM

Undifferentiated cells	88.0 nTPM
Small intestine	91.5 nTPM
Colon	91.1 nTPM
Rectum	81.4 nTPM

Amygdala excitatory	28.5 nTPM
Hippocampus	38.3 nTPM
Thalamus	36.3 nTPM
Cerebral cortex	33.7 nTPM
Amygdala	28.3 nTPM
Basal ganglia	23.6 nTPM
Hypothalamus	10.7 nTPM

Astrocyte	52.9 nTPM
Hypothalamus	112.9 nTPM
Amygdala	87.7 nTPM
Cerebral cortex	74.6 nTPM
Basal ganglia	66.2 nTPM
Hippocampus	56.7 nTPM
Pons	35.6 nTPM
Thalamus	33.8 nTPM
Midbrain	32.9 nTPM
Medulla oblongata	32.1 nTPM
Cerebellum	26.6 nTPM
Spinal cord	22.8 nTPM

Bergmann glia	41.9 nTPM
Medulla oblongata	44.8 nTPM
Cerebellum	40.7 nTPM
Pons	40.3 nTPM

Central nervous system macrophage	19.3 nTPM
Pons	21.9 nTPM
Hippocampus	21.1 nTPM
Basal ganglia	20.4 nTPM
Cerebral cortex	20.4 nTPM
Hypothalamus	20.0 nTPM
Amygdala	19.5 nTPM
Midbrain	19.5 nTPM
Thalamus	18.5 nTPM
Medulla oblongata	17.7 nTPM
Cerebellum	17.0 nTPM
Spinal cord	16.2 nTPM

Cerebellar inhibitory	60.5 nTPM
Midbrain	70.3 nTPM
Pons	66.8 nTPM
Cerebellum	58.8 nTPM
Spinal cord	55.0 nTPM
Medulla oblongata	51.7 nTPM

Cge interneuron	46.4 nTPM
Thalamus	76.9 nTPM
Midbrain	64.6 nTPM
Hippocampus	42.8 nTPM
Basal ganglia	42.6 nTPM
Cerebral cortex	42.6 nTPM
Amygdala	34.3 nTPM
Hypothalamus	20.7 nTPM

Choroid plexus epithelial cell	129.9 nTPM
Hippocampus	191.4 nTPM
Medulla oblongata	129.7 nTPM
Thalamus	106.9 nTPM
Basal ganglia	91.6 nTPM

Committed oligodendrocyte precursor	32.7 nTPM
Medulla oblongata	60.7 nTPM
Cerebellum	47.6 nTPM
Midbrain	38.6 nTPM
Hippocampus	38.5 nTPM
Pons	33.6 nTPM
Spinal cord	33.1 nTPM
Basal ganglia	30.7 nTPM
Cerebral cortex	26.6 nTPM
Thalamus	18.7 nTPM
Hypothalamus	16.4 nTPM
Amygdala	15.2 nTPM

Deep-layer corticothalamic and 6b	20.9 nTPM
Midbrain	37.7 nTPM
Hippocampus	23.5 nTPM
Basal ganglia	20.2 nTPM
Cerebral cortex	20.0 nTPM
Amygdala	14.7 nTPM
Hypothalamus	9.3 nTPM

Deep-layer intratelencephalic	19.8 nTPM
Cerebral cortex	26.5 nTPM
Basal ganglia	25.8 nTPM
Hippocampus	18.8 nTPM
Amygdala	16.2 nTPM
Hypothalamus	11.7 nTPM

Deep-layer near-projecting	34.1 nTPM
Basal ganglia	47.2 nTPM
Hippocampus	38.1 nTPM
Cerebral cortex	36.9 nTPM
Hypothalamus	24.8 nTPM
Amygdala	23.4 nTPM

Eccentric medium spiny neuron	27.0 nTPM
Hippocampus	29.4 nTPM
Basal ganglia	28.0 nTPM
Hypothalamus	26.4 nTPM
Amygdala	26.3 nTPM
Thalamus	26.2 nTPM
Cerebral cortex	25.6 nTPM