Single cell type - PHTF2 - The Human Protein Atlas

PHTF2

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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.	PHTF2
Gene descriptionⁱ Full gene name according to HGNC.	Putative homeodomain transcription factor 2
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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	8

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.	NK-cells & T-cells - Immune system & Transcription (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 (Oligodendrocytes, Monocytes, Excitatory neurons, Inhibitory neurons)
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.	0.45
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.	Immune cell enhanced (non-classical monocyte)
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 (Oligodendrocytes, Monocytes, Excitatory neurons, Inhibitory neurons)

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: Immune cell enhanced (non-classical monocyte)
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

PHTF2 is part of cluster 78 NK-cells & T-cells - Immune system & Transcription with confidenceⁱ 1
392 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.
STAM	Signal transducing adaptor molecule	0.5418	78
ZC3H12D	Zinc finger CCCH-type containing 12D	0.5198	78
TTC33	Tetratricopeptide repeat domain 33	0.5172	78
PPP1R16B	Protein phosphatase 1 regulatory subunit 16B	0.5110	78
CCR6	C-C motif chemokine receptor 6	0.5009	7
PBX4	PBX homeobox 4	0.4996	78
UHRF2	Ubiquitin like with PHD and ring finger domains 2	0.4945	78
CTLA4	Cytotoxic T-lymphocyte associated protein 4	0.4932	78
ZNF831	Zinc finger protein 831	0.4918	78
RHOH	Ras homolog family member H	0.4911	78
DUSP16	Dual specificity phosphatase 16	0.4900	78
CEP120	Centrosomal protein 120	0.4888	78
BORCS5	BLOC-1 related complex subunit 5	0.4843	78
CCR4	C-C motif chemokine receptor 4	0.4842	78
CCR8	C-C motif chemokine receptor 8	0.4743	78

IMMUNE CELLS

PHTF2 is part of cluster 42 Non-specific - Vesicular transport with confidenceⁱ 0.98
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.
MOSMO	Modulator of smoothened	1.0000	42
CNBD2	Cyclic nucleotide binding domain containing 2	0.9762	42
ARMH3	Armadillo like helical domain containing 3	0.9762	42
MED29	Mediator complex subunit 29	0.9524	42
TANGO2	Transport and golgi organization 2 homolog	0.9524	42
UBQLN1	Ubiquilin 1	0.9524	42
WDR11	WD repeat domain 11	0.9524	42
MANBA	Mannosidase beta	0.9524	42
CPEB3	Cytoplasmic polyadenylation element binding protein 3	0.9524	42
PRDM4	PR/SET domain 4	0.9286	42
SH3BGRL	SH3 domain binding glutamate rich protein like	0.9286	42
PNPLA8	Patatin like phospholipase domain containing 8	0.9286	42
PTGES	Prostaglandin E synthase	0.9286	42
GBF1	Golgi brefeldin A resistant guanine nucleotide exchange factor 1	0.9286	42
PSMC2	Proteasome 26S subunit, ATPase 2	0.9286	42

Adipocytes	11.6 nTPM
Adipose tissue	13.8 nTPM
Breast	9.3 nTPM

Alveolar cells type 1	5.9 nTPM
Lung	5.9 nTPM

Alveolar cells type 2	8.2 nTPM
Lung	8.2 nTPM

Astrocytes	30.0 nTPM
Brain	30.0 nTPM

B-cells	53.7 nTPM
Spleen	85.4 nTPM
Stomach	82.7 nTPM
Lymph node	76.6 nTPM
Adipose tissue	74.5 nTPM
Esophagus	70.8 nTPM
Bone marrow	61.6 nTPM
Thymus	47.7 nTPM
Salivary gland	39.4 nTPM
Lung	37.6 nTPM
Skin	37.3 nTPM
PBMC	33.9 nTPM
Kidney	26.0 nTPM
Liver	24.2 nTPM

Ciliated cells	7.5 nTPM
Bronchus	8.4 nTPM
Endometrium	8.3 nTPM
Lung	6.8 nTPM
Fallopian tube	6.7 nTPM

Club cells	12.2 nTPM
Prostate	13.6 nTPM
Bronchus	11.9 nTPM
Lung	11.1 nTPM

Dendritic cells	11.5 nTPM
Adipose tissue	12.2 nTPM
PBMC	10.8 nTPM

Endothelial cells	12.6 nTPM
Heart muscle	28.4 nTPM
Vascular	17.9 nTPM
Liver	17.6 nTPM
Esophagus	16.9 nTPM
Thymus	13.7 nTPM
Endometrium	12.5 nTPM
Salivary gland	12.5 nTPM
Skeletal muscle	12.4 nTPM
Breast	12.3 nTPM
Skin	12.0 nTPM
Tongue	11.5 nTPM
Prostate	11.1 nTPM
Testis	10.7 nTPM
Pancreas	10.3 nTPM
Fallopian tube	8.5 nTPM
Ovary	8.3 nTPM
Lung	6.4 nTPM
Placenta	3.4 nTPM

Enteroendocrine cells	7.2 nTPM
Small intestine	10.3 nTPM
Colon	6.4 nTPM
Rectum	5.0 nTPM

Fibroblasts	17.4 nTPM
Liver	28.5 nTPM
Pancreas	24.4 nTPM
Adipose tissue	23.5 nTPM
Fallopian tube	21.4 nTPM
Stomach	20.2 nTPM
Skeletal muscle	18.3 nTPM
Placenta	18.2 nTPM
Prostate	17.8 nTPM
Vascular	17.6 nTPM
Skin	15.1 nTPM
Esophagus	14.6 nTPM
Breast	14.2 nTPM
Salivary gland	13.8 nTPM
Thymus	12.7 nTPM
Heart muscle	9.3 nTPM
Lung	8.5 nTPM

Granulocytes	61.0 nTPM
Lung	65.0 nTPM
Tongue	63.1 nTPM
Fallopian tube	55.0 nTPM

Intestinal goblet cells	6.5 nTPM
Small intestine	8.2 nTPM
Rectum	6.3 nTPM
Colon	5.2 nTPM

Lymphatic endothelial cells	14.4 nTPM
Fallopian tube	17.9 nTPM
Ovary	10.9 nTPM

Macrophages	32.9 nTPM
Esophagus	45.0 nTPM
Spleen	44.1 nTPM
Adipose tissue	43.8 nTPM
Vascular	43.5 nTPM
Bone marrow	40.5 nTPM
Fallopian tube	40.5 nTPM
Stomach	38.6 nTPM
Tongue	36.7 nTPM
Kidney	35.4 nTPM
Skeletal muscle	33.2 nTPM
Thymus	30.7 nTPM
Endometrium	28.9 nTPM
Testis	28.5 nTPM
Salivary gland	28.4 nTPM
Skin	27.9 nTPM
Prostate	26.8 nTPM
Lung	26.0 nTPM
Breast	17.7 nTPM
Pancreas	8.2 nTPM

Basal keratinocytes	17.2 nTPM
Skin	19.6 nTPM
Tongue	14.7 nTPM

Basal squamous epithelial cells	16.8 nTPM
Esophagus	16.8 nTPM

Bipolar cells	8.9 nTPM
Eye	8.9 nTPM

Cholangiocytes	11.4 nTPM
Liver	11.4 nTPM

Paneth cells	7.0 nTPM
Colon	10.9 nTPM
Rectum	10.2 nTPM
Small intestine	0.0 nTPM

Plasma cells	27.2 nTPM
Spleen	55.3 nTPM
Bone marrow	40.8 nTPM
Thymus	31.9 nTPM
Stomach	23.5 nTPM
Esophagus	20.8 nTPM
Liver	20.5 nTPM
Salivary gland	13.9 nTPM
Fallopian tube	10.6 nTPM

Schwann cells	10.7 nTPM
Adipose tissue	20.7 nTPM
Vascular	11.5 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	12.3 nTPM
Tongue	17.7 nTPM
Salivary gland	6.9 nTPM

Smooth muscle cells	12.5 nTPM
Vascular	23.0 nTPM
Endometrium	22.6 nTPM
Placenta	16.0 nTPM
Adipose tissue	16.0 nTPM
Skin	15.1 nTPM
Thymus	12.9 nTPM
Prostate	12.8 nTPM
Breast	12.1 nTPM
Skeletal muscle	11.9 nTPM
Salivary gland	11.6 nTPM
Fallopian tube	10.7 nTPM
Ovary	10.1 nTPM
Tongue	8.7 nTPM
Liver	7.2 nTPM
Lung	5.9 nTPM
Esophagus	3.6 nTPM

Suprabasal keratinocytes	16.1 nTPM
Skin	17.0 nTPM
Tongue	15.1 nTPM

T-cells	49.4 nTPM
Skin	101.3 nTPM
Adipose tissue	99.5 nTPM
Stomach	71.6 nTPM
Esophagus	70.6 nTPM
Tongue	67.5 nTPM
Lymph node	67.2 nTPM
Spleen	66.6 nTPM
Skeletal muscle	61.2 nTPM
Vascular	54.7 nTPM
Bone marrow	50.8 nTPM
Fallopian tube	48.5 nTPM
Thymus	41.8 nTPM
Breast	41.1 nTPM
Endometrium	37.8 nTPM
Lung	35.8 nTPM
Colon	25.3 nTPM
Prostate	24.7 nTPM
Salivary gland	22.5 nTPM
Liver	18.0 nTPM
PBMC	16.6 nTPM
Kidney	14.2 nTPM

Undifferentiated cells	6.0 nTPM
Rectum	7.5 nTPM
Colon	7.1 nTPM
Small intestine	3.5 nTPM

Amygdala excitatory	153.6 nTPM
Cerebral cortex	159.6 nTPM
Hypothalamus	158.4 nTPM
Thalamus	158.4 nTPM
Amygdala	154.6 nTPM
Hippocampus	147.8 nTPM
Basal ganglia	143.2 nTPM

Astrocyte	55.0 nTPM
Amygdala	78.5 nTPM
Cerebral cortex	65.5 nTPM
Basal ganglia	61.4 nTPM
Hypothalamus	61.4 nTPM
Hippocampus	59.3 nTPM
Thalamus	55.0 nTPM
Midbrain	49.2 nTPM
Pons	46.9 nTPM
Spinal cord	45.5 nTPM
Medulla oblongata	41.5 nTPM
Cerebellum	40.3 nTPM

Bergmann glia	66.1 nTPM
Cerebellum	71.0 nTPM
Medulla oblongata	63.9 nTPM
Pons	63.3 nTPM

Central nervous system macrophage	159.2 nTPM
Amygdala	205.0 nTPM
Hypothalamus	181.9 nTPM
Basal ganglia	178.8 nTPM
Hippocampus	167.7 nTPM
Midbrain	164.5 nTPM
Cerebral cortex	152.3 nTPM
Cerebellum	150.5 nTPM
Thalamus	147.7 nTPM
Pons	144.3 nTPM
Medulla oblongata	134.9 nTPM
Spinal cord	123.6 nTPM

Cerebellar inhibitory	117.3 nTPM
Midbrain	128.8 nTPM
Spinal cord	123.7 nTPM
Pons	115.6 nTPM
Medulla oblongata	111.0 nTPM
Cerebellum	107.6 nTPM

Cge interneuron	110.7 nTPM
Amygdala	123.2 nTPM
Hypothalamus	121.1 nTPM
Thalamus	109.7 nTPM
Basal ganglia	109.3 nTPM
Cerebral cortex	105.7 nTPM
Hippocampus	103.7 nTPM
Midbrain	102.4 nTPM

Choroid plexus epithelial cell	71.8 nTPM
Basal ganglia	97.9 nTPM
Thalamus	79.5 nTPM
Medulla oblongata	73.9 nTPM
Hippocampus	36.1 nTPM

Committed oligodendrocyte precursor	189.0 nTPM
Cerebellum	241.0 nTPM
Hippocampus	232.8 nTPM
Hypothalamus	224.6 nTPM
Amygdala	223.3 nTPM
Cerebral cortex	216.6 nTPM
Midbrain	203.3 nTPM
Pons	181.5 nTPM
Thalamus	152.6 nTPM
Spinal cord	150.8 nTPM
Basal ganglia	145.6 nTPM
Medulla oblongata	107.2 nTPM

Deep-layer corticothalamic and 6b	145.0 nTPM
Midbrain	168.6 nTPM
Basal ganglia	145.4 nTPM
Hypothalamus	142.4 nTPM
Cerebral cortex	139.8 nTPM
Amygdala	138.4 nTPM
Hippocampus	135.5 nTPM

Deep-layer intratelencephalic	144.5 nTPM
Amygdala	166.9 nTPM
Basal ganglia	150.3 nTPM
Cerebral cortex	136.7 nTPM
Hippocampus	135.4 nTPM
Hypothalamus	133.4 nTPM

Deep-layer near-projecting	136.6 nTPM
Cerebral cortex	140.7 nTPM
Amygdala	139.7 nTPM
Basal ganglia	136.9 nTPM
Hypothalamus	136.3 nTPM
Hippocampus	129.4 nTPM

Eccentric medium spiny neuron	162.6 nTPM
Basal ganglia	174.6 nTPM
Amygdala	174.3 nTPM
Thalamus	170.1 nTPM
Cerebral cortex	166.5 nTPM
Hypothalamus	147.9 nTPM
Hippocampus	142.2 nTPM