Single cell type - PHF7 - The Human Protein Atlas

PHF7

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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.	PHF7
Gene descriptionⁱ Full gene name according to HGNC.	PHD finger protein 7
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.	5

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 - 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.	Group enriched (Late spermatids, 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.	0.77
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: Group enriched (Late spermatids, 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

PHF7 is part of cluster 63 Late spermatids - Spermatogenesis with confidenceⁱ 1
383 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.
TSACC	TSSK6 activating cochaperone	0.9140	63
ODF2	Outer dense fiber of sperm tails 2	0.9100	63
C5orf52	Chromosome 5 open reading frame 52	0.9087	63
CCDC70	Coiled-coil domain containing 70	0.9023	63
C10orf53	Chromosome 10 open reading frame 53	0.9020	63
PRM2	Protamine 2	0.8953	63
C16orf78	Chromosome 16 open reading frame 78	0.8917	63
ACTRT2	Actin related protein T2	0.8886	63
IQCF3	IQ motif containing F3	0.8875	63
AKAP4	A-kinase anchoring protein 4	0.8871	63
CLCNKA	Chloride voltage-gated channel Ka	0.8808	63
C11orf42	Chromosome 11 open reading frame 42	0.8807	63
PRM3	Protamine 3	0.8746	63
ENSG00000261341	Novel protein	0.8730	63
YJEFN3	YjeF N-terminal domain containing 3	0.8636	63

IMMUNE CELLS

PHF7 is part of cluster 14 Non-specific - Unknown function with confidenceⁱ 0.99
292 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.
ENSG00000261341	Novel protein	0.9762	14
TRMT61B	TRNA methyltransferase 61B	0.9524	14
EFNA3	Ephrin A3	0.9524	14
SELENOI	Selenoprotein I	0.9524	14
ITFG2	Integrin alpha FG-GAP repeat containing 2	0.9524	14
CCT6B	Chaperonin containing TCP1 subunit 6B	0.9524	14
PRDX4	Peroxiredoxin 4	0.9524	14
RBM19	RNA binding motif protein 19	0.9524	14
UTP25	UTP25 small subunit processome component	0.9286	14
SSBP4	Single stranded DNA binding protein 4	0.9286	23
MORN1	MORN repeat containing 1	0.9286	33
MSH3	MutS homolog 3	0.9286	14
DHX35	DEAH-box helicase 35	0.9286	14
SLC17A9	Solute carrier family 17 member 9	0.9286	14
DNAL1	Dynein axonemal light chain 1	0.9048	14

Adipocytes	4.2 nTPM
Adipose tissue	4.2 nTPM
Breast	4.2 nTPM

Alveolar cells type 1	1.5 nTPM
Lung	1.5 nTPM

Alveolar cells type 2	2.8 nTPM
Lung	2.8 nTPM

Astrocytes	14.9 nTPM
Brain	14.9 nTPM

B-cells	8.5 nTPM
Liver	19.3 nTPM
Esophagus	17.7 nTPM
Bone marrow	12.0 nTPM
Lymph node	10.1 nTPM
Stomach	9.7 nTPM
Lung	8.0 nTPM
Adipose tissue	7.0 nTPM
Thymus	6.6 nTPM
Salivary gland	6.3 nTPM
PBMC	6.2 nTPM
Spleen	6.0 nTPM
Skin	1.7 nTPM
Kidney	0.0 nTPM

Ciliated cells	6.6 nTPM
Lung	10.1 nTPM
Fallopian tube	6.7 nTPM
Endometrium	5.3 nTPM
Bronchus	4.2 nTPM

Club cells	3.6 nTPM
Prostate	5.4 nTPM
Bronchus	2.9 nTPM
Lung	2.6 nTPM

Endothelial cells	4.4 nTPM
Testis	33.6 nTPM
Skeletal muscle	5.9 nTPM
Esophagus	4.7 nTPM
Prostate	3.6 nTPM
Placenta	3.4 nTPM
Thymus	3.2 nTPM
Vascular	3.2 nTPM
Heart muscle	2.7 nTPM
Liver	2.5 nTPM
Lung	2.5 nTPM
Fallopian tube	2.5 nTPM
Ovary	2.2 nTPM
Tongue	2.1 nTPM
Salivary gland	2.0 nTPM
Breast	1.8 nTPM
Skin	1.7 nTPM
Endometrium	1.3 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	7.9 nTPM
Rectum	15.1 nTPM
Colon	8.7 nTPM
Small intestine	0.0 nTPM

Fibroblasts	4.9 nTPM
Esophagus	11.7 nTPM
Heart muscle	9.0 nTPM
Adipose tissue	8.3 nTPM
Stomach	7.2 nTPM
Skeletal muscle	6.4 nTPM
Salivary gland	6.4 nTPM
Breast	4.1 nTPM
Thymus	3.9 nTPM
Liver	3.6 nTPM
Skin	3.4 nTPM
Prostate	3.3 nTPM
Vascular	3.0 nTPM
Fallopian tube	3.0 nTPM
Placenta	2.1 nTPM
Pancreas	2.1 nTPM
Lung	1.8 nTPM

Granulocytes	9.7 nTPM
Tongue	19.4 nTPM
Lung	6.1 nTPM
Fallopian tube	3.8 nTPM

Intestinal goblet cells	4.4 nTPM
Rectum	5.5 nTPM
Colon	3.9 nTPM
Small intestine	3.7 nTPM

Lymphatic endothelial cells	1.3 nTPM
Fallopian tube	2.6 nTPM
Ovary	0.0 nTPM

Macrophages	5.4 nTPM
Testis	37.2 nTPM
Spleen	7.0 nTPM
Breast	6.1 nTPM
Bone marrow	5.1 nTPM
Adipose tissue	4.3 nTPM
Prostate	4.3 nTPM
Lung	3.9 nTPM
Endometrium	3.7 nTPM
Tongue	3.7 nTPM
Fallopian tube	3.7 nTPM
Skeletal muscle	3.4 nTPM
Salivary gland	3.4 nTPM
Vascular	3.4 nTPM
Skin	3.3 nTPM
Thymus	2.7 nTPM
Stomach	2.6 nTPM
Pancreas	2.1 nTPM
Kidney	1.8 nTPM
Esophagus	1.3 nTPM

Paneth cells	4.4 nTPM
Small intestine	6.9 nTPM
Rectum	6.3 nTPM
Colon	0.0 nTPM

Basal squamous epithelial cells	9.3 nTPM
Esophagus	9.3 nTPM

Bipolar cells	8.8 nTPM
Eye	8.8 nTPM

Collecting duct cells	5.8 nTPM
Kidney	5.8 nTPM

Cone photoreceptor cells	11.9 nTPM
Eye	11.9 nTPM

Plasma cells	6.3 nTPM
Liver	10.0 nTPM
Bone marrow	9.1 nTPM
Thymus	9.1 nTPM
Stomach	8.4 nTPM
Fallopian tube	6.1 nTPM
Spleen	6.0 nTPM
Salivary gland	1.8 nTPM
Esophagus	0.0 nTPM

Schwann cells	2.0 nTPM
Vascular	3.1 nTPM
Adipose tissue	2.7 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	4.7 nTPM
Salivary gland	4.9 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	4.9 nTPM
Esophagus	9.6 nTPM
Skeletal muscle	9.1 nTPM
Breast	6.7 nTPM
Ovary	6.6 nTPM
Skin	5.2 nTPM
Tongue	5.1 nTPM
Prostate	4.9 nTPM
Lung	4.7 nTPM
Adipose tissue	4.2 nTPM
Salivary gland	4.0 nTPM
Liver	3.4 nTPM
Endometrium	3.4 nTPM
Fallopian tube	3.4 nTPM
Vascular	3.3 nTPM
Placenta	2.8 nTPM
Thymus	2.7 nTPM

T-cells	5.4 nTPM
Esophagus	12.2 nTPM
Lymph node	10.4 nTPM
Bone marrow	8.0 nTPM
Liver	7.1 nTPM
PBMC	7.1 nTPM
Salivary gland	6.7 nTPM
Skin	6.0 nTPM
Thymus	5.1 nTPM
Adipose tissue	4.6 nTPM
Skeletal muscle	4.5 nTPM
Spleen	4.5 nTPM
Lung	4.5 nTPM
Tongue	4.5 nTPM
Kidney	4.4 nTPM
Stomach	4.4 nTPM
Breast	4.0 nTPM
Colon	3.9 nTPM
Prostate	3.3 nTPM
Vascular	3.2 nTPM
Fallopian tube	3.1 nTPM
Endometrium	2.2 nTPM

Undifferentiated cells	9.7 nTPM
Rectum	11.6 nTPM
Small intestine	9.0 nTPM
Colon	8.4 nTPM

Amygdala excitatory	15.8 nTPM
Hypothalamus	19.1 nTPM
Cerebral cortex	18.0 nTPM
Hippocampus	16.4 nTPM
Amygdala	16.2 nTPM
Basal ganglia	16.2 nTPM
Thalamus	8.6 nTPM

Astrocyte	26.9 nTPM
Cerebral cortex	31.5 nTPM
Hippocampus	30.7 nTPM
Thalamus	30.2 nTPM
Midbrain	30.1 nTPM
Amygdala	28.4 nTPM
Basal ganglia	27.3 nTPM
Pons	26.2 nTPM
Spinal cord	25.4 nTPM
Medulla oblongata	22.8 nTPM
Hypothalamus	22.0 nTPM
Cerebellum	21.6 nTPM

Bergmann glia	25.5 nTPM
Pons	31.6 nTPM
Cerebellum	23.6 nTPM
Medulla oblongata	21.3 nTPM

Central nervous system macrophage	16.8 nTPM
Spinal cord	18.5 nTPM
Cerebral cortex	18.4 nTPM
Hippocampus	17.7 nTPM
Medulla oblongata	17.5 nTPM
Cerebellum	17.3 nTPM
Basal ganglia	16.9 nTPM
Midbrain	16.8 nTPM
Pons	16.0 nTPM
Hypothalamus	15.9 nTPM
Thalamus	15.1 nTPM
Amygdala	14.3 nTPM

Cerebellar inhibitory	28.9 nTPM
Cerebellum	31.9 nTPM
Spinal cord	30.2 nTPM
Pons	28.9 nTPM
Midbrain	28.3 nTPM
Medulla oblongata	25.0 nTPM

Cge interneuron	10.8 nTPM
Hypothalamus	11.9 nTPM
Cerebral cortex	11.8 nTPM
Midbrain	11.4 nTPM
Hippocampus	11.2 nTPM
Basal ganglia	10.6 nTPM
Amygdala	9.7 nTPM
Thalamus	8.9 nTPM

Choroid plexus epithelial cell	14.2 nTPM
Basal ganglia	21.4 nTPM
Medulla oblongata	16.0 nTPM
Thalamus	11.0 nTPM
Hippocampus	8.3 nTPM

Committed oligodendrocyte precursor	14.8 nTPM
Hypothalamus	25.3 nTPM
Thalamus	24.5 nTPM
Midbrain	16.8 nTPM
Cerebral cortex	16.5 nTPM
Hippocampus	14.7 nTPM
Spinal cord	14.7 nTPM
Basal ganglia	12.6 nTPM
Amygdala	11.3 nTPM
Pons	9.7 nTPM
Medulla oblongata	9.0 nTPM
Cerebellum	7.9 nTPM

Deep-layer corticothalamic and 6b	17.6 nTPM
Hippocampus	18.5 nTPM
Hypothalamus	18.3 nTPM
Midbrain	17.8 nTPM
Basal ganglia	17.3 nTPM
Cerebral cortex	17.3 nTPM
Amygdala	16.6 nTPM

Deep-layer intratelencephalic	19.9 nTPM
Hypothalamus	22.8 nTPM
Basal ganglia	21.5 nTPM
Cerebral cortex	19.5 nTPM
Hippocampus	19.5 nTPM
Amygdala	16.0 nTPM

Deep-layer near-projecting	19.5 nTPM
Basal ganglia	21.5 nTPM
Hippocampus	20.8 nTPM
Cerebral cortex	18.9 nTPM
Hypothalamus	18.8 nTPM
Amygdala	17.7 nTPM

Eccentric medium spiny neuron	17.4 nTPM
Hypothalamus	20.5 nTPM
Basal ganglia	18.6 nTPM
Cerebral cortex	17.9 nTPM
Thalamus	17.5 nTPM
Amygdala	15.0 nTPM
Hippocampus	14.9 nTPM

Endothelial cell	8.3 nTPM
Hippocampus	15.7 nTPM
Cerebellum	10.8 nTPM
Midbrain	10.4 nTPM
Spinal cord	10.4 nTPM
Cerebral cortex	10.2 nTPM
Basal ganglia	8.4 nTPM
Hypothalamus	7.4 nTPM
Pons	6.9 nTPM
Thalamus	6.2 nTPM
Amygdala	3.4 nTPM
Medulla oblongata	2.1 nTPM

Ependymal cell	26.4 nTPM
Hippocampus	35.6 nTPM
Amygdala	35.3 nTPM
Pons	28.7 nTPM
Spinal cord	28.7 nTPM
Basal ganglia	26.1 nTPM
Hypothalamus	25.0 nTPM
Medulla oblongata	22.6 nTPM
Midbrain	20.3 nTPM
Thalamus	15.4 nTPM