Single cell type - GHITM - The Human Protein Atlas

GHITM

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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.	GHITM
Gene descriptionⁱ Full gene name according to HGNC.	Growth hormone inducible transmembrane protein
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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	10

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.	Late spermatids - Unknown 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 (Late spermatids, Cardiomyocytes, Early 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.	0.36
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 (Late spermatids, Cardiomyocytes, Early 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

GHITM is part of cluster 36 Late spermatids - Unknown function with confidenceⁱ 1
427 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.
UQCRC1	Ubiquinol-cytochrome c reductase core protein 1	0.6031	39
RAB1A	RAB1A, member RAS oncogene family	0.5721	36
STAMBP	STAM binding protein	0.5387	36
NDUFS2	NADH:ubiquinone oxidoreductase core subunit S2	0.5361	39
ATP5F1C	ATP synthase F1 subunit gamma	0.5275	39
CIB1	Calcium and integrin binding 1	0.5194	45
NDUFB9	NADH:ubiquinone oxidoreductase subunit B9	0.5186	15
SHBG	Sex hormone binding globulin	0.5185	36
UBE2N	Ubiquitin conjugating enzyme E2 N	0.5161	36
ELOB	Elongin B	0.5087	63
MORN2	MORN repeat containing 2	0.5036	36
MPC2	Mitochondrial pyruvate carrier 2	0.5010	36
NDUFA9	NADH:ubiquinone oxidoreductase subunit A9	0.4982	63
NDUFA1	NADH:ubiquinone oxidoreductase subunit A1	0.4981	39
ENSG00000267618	RAD51L3-RFFL readthrough	0.4970	36

IMMUNE CELLS

GHITM is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 0.92
501 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.
INIP	INTS3 and NABP interacting protein	0.9762	38
BECN1	Beclin 1	0.9762	42
GRIPAP1	GRIP1 associated protein 1	0.9524	38
ZNF655	Zinc finger protein 655	0.9286	42
PSMD6	Proteasome 26S subunit, non-ATPase 6	0.9286	42
ARPC2	Actin related protein 2/3 complex subunit 2	0.9286	38
UBE2L6	Ubiquitin conjugating enzyme E2 L6	0.9286	37
DDX5	DEAD-box helicase 5	0.9286	42
FUCA2	Alpha-L-fucosidase 2	0.9286	38
RNF114	Ring finger protein 114	0.9286	10
RAB14	RAB14, member RAS oncogene family	0.9048	40
LGALS3	Galectin 3	0.9048	38
FLVCR2	FLVCR heme transporter 2	0.9048	40
ACTR3	Actin related protein 3	0.9048	40
CSNK1A1	Casein kinase 1 alpha 1	0.9048	42

Adipocytes	91.9 nTPM
Breast	92.9 nTPM
Adipose tissue	90.9 nTPM

Alveolar cells type 1	173.5 nTPM
Lung	173.5 nTPM

Alveolar cells type 2	178.7 nTPM
Lung	178.7 nTPM

Astrocytes	22.0 nTPM
Brain	22.0 nTPM

B-cells	112.0 nTPM
Kidney	150.8 nTPM
Skin	150.8 nTPM
Lung	134.1 nTPM
Stomach	125.3 nTPM
Spleen	120.1 nTPM
PBMC	117.0 nTPM
Adipose tissue	116.0 nTPM
Bone marrow	108.4 nTPM
Lymph node	102.4 nTPM
Thymus	97.6 nTPM
Salivary gland	90.9 nTPM
Liver	77.3 nTPM
Esophagus	64.9 nTPM

Basal squamous epithelial cells	109.3 nTPM
Esophagus	109.3 nTPM

Ciliated cells	120.1 nTPM
Bronchus	208.2 nTPM
Lung	112.8 nTPM
Fallopian tube	98.6 nTPM
Endometrium	60.8 nTPM

Club cells	185.7 nTPM
Bronchus	333.4 nTPM
Lung	121.4 nTPM
Prostate	102.3 nTPM

Dendritic cells	134.0 nTPM
Adipose tissue	149.3 nTPM
PBMC	118.7 nTPM

Endothelial cells	114.6 nTPM
Heart muscle	239.4 nTPM
Pancreas	206.8 nTPM
Skin	135.7 nTPM
Testis	130.9 nTPM
Placenta	127.7 nTPM
Lung	123.8 nTPM
Tongue	121.7 nTPM
Breast	116.0 nTPM
Fallopian tube	110.1 nTPM
Liver	100.8 nTPM
Skeletal muscle	99.3 nTPM
Thymus	95.2 nTPM
Prostate	89.9 nTPM
Ovary	87.9 nTPM
Salivary gland	77.7 nTPM
Vascular	73.0 nTPM
Esophagus	67.8 nTPM
Endometrium	59.3 nTPM

Enteroendocrine cells	186.2 nTPM
Colon	344.5 nTPM
Small intestine	120.2 nTPM
Rectum	93.9 nTPM

Erythroid cells	162.9 nTPM
Liver	230.7 nTPM
Bone marrow	95.0 nTPM

Fibroblasts	122.7 nTPM
Heart muscle	317.5 nTPM
Pancreas	250.8 nTPM
Placenta	125.5 nTPM
Lung	121.7 nTPM
Adipose tissue	114.3 nTPM
Fallopian tube	114.0 nTPM
Skin	112.6 nTPM
Thymus	96.0 nTPM
Esophagus	95.2 nTPM
Breast	94.5 nTPM
Skeletal muscle	93.1 nTPM
Prostate	91.7 nTPM
Vascular	89.6 nTPM
Salivary gland	86.0 nTPM
Liver	81.8 nTPM
Stomach	79.3 nTPM

Granulocytes	163.2 nTPM
Fallopian tube	190.8 nTPM
Lung	177.5 nTPM
Tongue	121.3 nTPM

Intestinal goblet cells	173.1 nTPM
Colon	231.8 nTPM
Rectum	191.7 nTPM
Small intestine	95.8 nTPM

Bipolar cells	130.1 nTPM
Eye	130.1 nTPM

Cholangiocytes	148.8 nTPM
Liver	148.8 nTPM

Collecting duct cells	163.4 nTPM
Kidney	163.4 nTPM

Cone photoreceptor cells	226.0 nTPM
Eye	226.0 nTPM

Lymphatic endothelial cells	113.1 nTPM
Fallopian tube	144.5 nTPM
Ovary	81.8 nTPM

Macrophages	144.8 nTPM
Pancreas	308.3 nTPM
Kidney	231.0 nTPM
Lung	201.2 nTPM
Adipose tissue	177.8 nTPM
Fallopian tube	162.4 nTPM
Testis	158.1 nTPM
Stomach	154.3 nTPM
Spleen	140.4 nTPM
Bone marrow	134.8 nTPM
Prostate	128.0 nTPM
Skeletal muscle	123.0 nTPM
Vascular	119.7 nTPM
Endometrium	119.3 nTPM
Thymus	118.0 nTPM
Tongue	113.4 nTPM
Salivary gland	103.7 nTPM
Breast	98.5 nTPM
Esophagus	82.2 nTPM
Skin	78.0 nTPM

Paneth cells	261.2 nTPM
Small intestine	300.5 nTPM
Colon	256.9 nTPM
Rectum	226.1 nTPM

Plasma cells	208.3 nTPM
Liver	302.4 nTPM
Thymus	284.9 nTPM
Spleen	258.6 nTPM
Stomach	201.4 nTPM
Fallopian tube	198.8 nTPM
Bone marrow	191.8 nTPM
Salivary gland	124.5 nTPM
Esophagus	104.0 nTPM

Schwann cells	99.4 nTPM
Adipose tissue	199.1 nTPM
Vascular	63.2 nTPM
Esophagus	35.9 nTPM

Serous glandular cells	131.5 nTPM
Salivary gland	143.7 nTPM
Tongue	119.3 nTPM

Smooth muscle cells	120.3 nTPM
Skin	161.7 nTPM
Ovary	148.3 nTPM
Fallopian tube	146.2 nTPM
Placenta	129.8 nTPM
Skeletal muscle	129.8 nTPM
Prostate	128.3 nTPM
Breast	125.4 nTPM
Esophagus	123.7 nTPM
Thymus	119.3 nTPM
Salivary gland	118.0 nTPM
Vascular	117.3 nTPM
Liver	110.4 nTPM
Lung	107.0 nTPM
Tongue	97.6 nTPM
Adipose tissue	95.5 nTPM
Endometrium	66.5 nTPM

Suprabasal keratinocytes	222.8 nTPM
Tongue	282.1 nTPM
Skin	163.5 nTPM

T-cells	128.7 nTPM
Kidney	213.7 nTPM
Fallopian tube	186.3 nTPM
Colon	166.7 nTPM
Stomach	162.2 nTPM
Liver	160.8 nTPM
Skin	156.3 nTPM
Adipose tissue	144.3 nTPM
Spleen	134.5 nTPM
Breast	129.9 nTPM
Bone marrow	125.0 nTPM
Lung	124.4 nTPM
Thymus	123.6 nTPM
Tongue	117.4 nTPM
PBMC	114.7 nTPM
Prostate	112.8 nTPM
Lymph node	111.5 nTPM
Skeletal muscle	102.1 nTPM
Salivary gland	88.3 nTPM
Esophagus	80.3 nTPM
Vascular	74.8 nTPM
Endometrium	73.1 nTPM

Undifferentiated cells	240.8 nTPM
Colon	289.4 nTPM
Rectum	218.2 nTPM
Small intestine	214.9 nTPM

Amygdala excitatory	32.3 nTPM
Hippocampus	37.4 nTPM
Basal ganglia	36.4 nTPM
Thalamus	33.1 nTPM
Cerebral cortex	31.1 nTPM
Hypothalamus	28.1 nTPM
Amygdala	27.6 nTPM

Astrocyte	22.7 nTPM
Thalamus	29.6 nTPM
Cerebellum	26.3 nTPM
Basal ganglia	25.4 nTPM
Cerebral cortex	25.4 nTPM
Pons	24.4 nTPM
Midbrain	22.8 nTPM
Hippocampus	20.9 nTPM
Hypothalamus	20.4 nTPM
Medulla oblongata	20.3 nTPM
Amygdala	19.2 nTPM
Spinal cord	14.8 nTPM

Bergmann glia	28.9 nTPM
Pons	36.0 nTPM
Medulla oblongata	25.6 nTPM
Cerebellum	25.1 nTPM

Central nervous system macrophage	27.9 nTPM
Hypothalamus	37.0 nTPM
Thalamus	33.5 nTPM
Cerebral cortex	29.8 nTPM
Pons	29.7 nTPM
Basal ganglia	27.7 nTPM
Medulla oblongata	27.2 nTPM
Amygdala	26.4 nTPM
Midbrain	25.9 nTPM
Spinal cord	25.3 nTPM
Hippocampus	23.5 nTPM
Cerebellum	21.0 nTPM

Cerebellar inhibitory	61.5 nTPM
Pons	81.9 nTPM
Midbrain	66.9 nTPM
Medulla oblongata	59.1 nTPM
Cerebellum	55.4 nTPM
Spinal cord	44.0 nTPM

Cge interneuron	47.6 nTPM
Thalamus	73.8 nTPM
Midbrain	52.9 nTPM
Hippocampus	47.3 nTPM
Basal ganglia	46.0 nTPM
Cerebral cortex	44.8 nTPM
Amygdala	37.2 nTPM
Hypothalamus	30.9 nTPM

Choroid plexus epithelial cell	55.2 nTPM
Hippocampus	74.9 nTPM
Thalamus	60.3 nTPM
Medulla oblongata	53.8 nTPM
Basal ganglia	31.8 nTPM

Committed oligodendrocyte precursor	24.4 nTPM
Medulla oblongata	46.5 nTPM
Thalamus	35.3 nTPM
Pons	34.5 nTPM
Basal ganglia	31.2 nTPM
Midbrain	26.0 nTPM
Hypothalamus	21.2 nTPM
Hippocampus	17.6 nTPM
Cerebellum	17.4 nTPM
Amygdala	16.4 nTPM
Cerebral cortex	15.2 nTPM
Spinal cord	7.4 nTPM

Deep-layer corticothalamic and 6b	44.8 nTPM
Midbrain	51.0 nTPM
Basal ganglia	47.9 nTPM
Hypothalamus	44.0 nTPM
Amygdala	42.8 nTPM
Cerebral cortex	42.4 nTPM
Hippocampus	40.3 nTPM

Deep-layer intratelencephalic	45.0 nTPM
Cerebral cortex	50.9 nTPM
Hypothalamus	47.0 nTPM
Hippocampus	46.9 nTPM
Basal ganglia	43.8 nTPM
Amygdala	36.4 nTPM