Single cell type - PHLDB1 - The Human Protein Atlas

PHLDB1

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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.	PHLDB1
Gene descriptionⁱ Full gene name according to HGNC.	Pleckstrin homology like domain family B member 1
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.	Endometrial stromal cells - 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, Late spermatids, Endometrial stromal cells)
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.	0.57
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.	Cell type enhanced (Oligodendrocyte, Committed oligodendrocyte precursor)
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.	Not detected in immune cells
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, Late spermatids, Endometrial stromal cells)

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: Cell type enhanced (Oligodendrocyte, Committed oligodendrocyte precursor)

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: Not detected in immune cells
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

PHLDB1 is part of cluster 9 Endometrial stromal cells - Transcription with confidenceⁱ 1
129 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.
GXYLT2	Glucoside xylosyltransferase 2	0.5314	53
PRRX1	Paired related homeobox 1	0.5119	53
RASSF8	Ras association domain family member 8	0.4908	11
PAPPA	Pappalysin 1	0.4890	9
INAFM1	InaF motif containing 1	0.4887	9
ANKRD13B	Ankyrin repeat domain 13B	0.4855	9
HOXA6	Homeobox A6	0.4714	9
CHODL	Chondrolectin	0.4546	9
PLEKHH2	Pleckstrin homology, MyTH4 and FERM domain containing H2	0.4540	9
VSTM4	V-set and transmembrane domain containing 4	0.4531	11
RAB3IL1	RAB3A interacting protein like 1	0.4504	11
IGF1	Insulin like growth factor 1	0.4457	9
APCDD1	APC down-regulated 1	0.4403	9
HIC1	HIC ZBTB transcriptional repressor 1	0.4392	53
GLI1	GLI family zinc finger 1	0.4390	9

Adipocytes	30.8 nTPM
Adipose tissue	32.8 nTPM
Breast	28.7 nTPM

Alveolar cells type 1	11.5 nTPM
Lung	11.5 nTPM

Alveolar cells type 2	5.1 nTPM
Lung	5.1 nTPM

Astrocytes	50.5 nTPM
Brain	50.5 nTPM

B-cells	2.0 nTPM
Skin	8.5 nTPM
Esophagus	5.9 nTPM
Thymus	3.3 nTPM
Spleen	2.1 nTPM
Salivary gland	1.7 nTPM
Adipose tissue	1.6 nTPM
Lymph node	1.6 nTPM
Stomach	1.3 nTPM
Bone marrow	0.7 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	7.9 nTPM
Fallopian tube	12.8 nTPM
Endometrium	12.4 nTPM
Lung	5.5 nTPM
Bronchus	1.0 nTPM

Club cells	3.5 nTPM
Lung	5.0 nTPM
Prostate	4.0 nTPM
Bronchus	1.6 nTPM

Endothelial cells	25.4 nTPM
Skeletal muscle	49.2 nTPM
Pancreas	46.5 nTPM
Lung	44.2 nTPM
Endometrium	34.8 nTPM
Placenta	32.4 nTPM
Skin	29.1 nTPM
Fallopian tube	27.6 nTPM
Thymus	26.9 nTPM
Ovary	25.0 nTPM
Salivary gland	23.4 nTPM
Tongue	22.1 nTPM
Vascular	20.3 nTPM
Esophagus	20.2 nTPM
Prostate	17.9 nTPM
Liver	11.3 nTPM
Heart muscle	9.7 nTPM
Testis	8.2 nTPM
Breast	7.9 nTPM

Enteroendocrine cells	9.0 nTPM
Colon	13.6 nTPM
Rectum	10.1 nTPM
Small intestine	3.4 nTPM

Fibroblasts	62.3 nTPM
Fallopian tube	132.3 nTPM
Skeletal muscle	94.9 nTPM
Thymus	91.8 nTPM
Stomach	82.1 nTPM
Salivary gland	79.8 nTPM
Vascular	78.9 nTPM
Adipose tissue	71.0 nTPM
Esophagus	63.5 nTPM
Skin	60.4 nTPM
Prostate	54.8 nTPM
Breast	54.5 nTPM
Pancreas	44.1 nTPM
Lung	38.8 nTPM
Liver	24.9 nTPM
Heart muscle	15.3 nTPM
Placenta	10.0 nTPM

Granulocytes	5.1 nTPM
Fallopian tube	8.5 nTPM
Tongue	4.9 nTPM
Lung	2.0 nTPM

Intestinal goblet cells	26.6 nTPM
Small intestine	37.2 nTPM
Rectum	26.6 nTPM
Colon	16.0 nTPM

Lymphatic endothelial cells	20.3 nTPM
Ovary	21.8 nTPM
Fallopian tube	18.8 nTPM

Macrophages	9.5 nTPM
Skeletal muscle	35.0 nTPM
Adipose tissue	21.4 nTPM
Fallopian tube	16.9 nTPM
Tongue	16.6 nTPM
Skin	15.6 nTPM
Endometrium	13.5 nTPM
Stomach	12.9 nTPM
Vascular	10.5 nTPM
Breast	8.7 nTPM
Thymus	7.6 nTPM
Esophagus	6.4 nTPM
Salivary gland	5.1 nTPM
Spleen	5.0 nTPM
Lung	2.3 nTPM
Prostate	1.7 nTPM
Testis	1.2 nTPM
Kidney	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM

Paneth cells	28.2 nTPM
Rectum	35.5 nTPM
Small intestine	31.1 nTPM
Colon	18.1 nTPM

Basal keratinocytes	12.1 nTPM
Skin	18.0 nTPM
Tongue	6.3 nTPM

Basal squamous epithelial cells	9.1 nTPM
Esophagus	9.1 nTPM

Bipolar cells	2.9 nTPM
Eye	2.9 nTPM

Cholangiocytes	3.8 nTPM
Liver	3.8 nTPM

Plasma cells	2.3 nTPM
Fallopian tube	10.9 nTPM
Salivary gland	3.1 nTPM
Thymus	3.0 nTPM
Liver	1.0 nTPM
Stomach	0.4 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Schwann cells	60.4 nTPM
Esophagus	107.8 nTPM
Vascular	71.6 nTPM
Adipose tissue	2.0 nTPM

Serous glandular cells	6.7 nTPM
Salivary gland	9.1 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	52.2 nTPM
Adipose tissue	85.7 nTPM
Skeletal muscle	80.9 nTPM
Tongue	77.2 nTPM
Esophagus	76.9 nTPM
Lung	61.1 nTPM
Endometrium	58.1 nTPM
Skin	57.6 nTPM
Thymus	55.5 nTPM
Vascular	50.0 nTPM
Placenta	45.2 nTPM
Breast	38.3 nTPM
Ovary	34.2 nTPM
Prostate	30.4 nTPM
Salivary gland	28.8 nTPM
Liver	28.0 nTPM
Fallopian tube	26.9 nTPM

T-cells	5.1 nTPM
Skin	20.7 nTPM
Colon	11.7 nTPM
Esophagus	9.7 nTPM
Breast	7.2 nTPM
Endometrium	6.5 nTPM
Skeletal muscle	6.0 nTPM
Adipose tissue	6.0 nTPM
Vascular	5.6 nTPM
Lymph node	5.4 nTPM
Tongue	5.0 nTPM
Salivary gland	3.5 nTPM
Spleen	3.3 nTPM
Fallopian tube	2.8 nTPM
Thymus	2.6 nTPM
Liver	2.5 nTPM
Lung	2.4 nTPM
Prostate	2.2 nTPM
PBMC	1.5 nTPM
Stomach	1.0 nTPM
Kidney	0.9 nTPM
Bone marrow	0.5 nTPM

Undifferentiated cells	12.6 nTPM
Rectum	20.2 nTPM
Colon	9.9 nTPM
Small intestine	7.6 nTPM

Amygdala excitatory	13.0 nTPM
Thalamus	25.4 nTPM
Basal ganglia	16.1 nTPM
Amygdala	11.5 nTPM
Hippocampus	9.2 nTPM
Hypothalamus	9.2 nTPM
Cerebral cortex	6.9 nTPM

Astrocyte	78.9 nTPM
Cerebellum	104.9 nTPM
Hippocampus	102.0 nTPM
Amygdala	94.0 nTPM
Midbrain	90.0 nTPM
Pons	84.2 nTPM
Cerebral cortex	83.2 nTPM
Thalamus	81.2 nTPM
Basal ganglia	68.9 nTPM
Spinal cord	54.7 nTPM
Hypothalamus	53.4 nTPM
Medulla oblongata	51.2 nTPM

Bergmann glia	30.9 nTPM
Cerebellum	41.0 nTPM
Pons	30.2 nTPM
Medulla oblongata	21.3 nTPM

Central nervous system macrophage	7.0 nTPM
Spinal cord	16.2 nTPM
Midbrain	11.1 nTPM
Hippocampus	9.0 nTPM
Cerebellum	7.5 nTPM
Pons	6.2 nTPM
Cerebral cortex	5.9 nTPM
Amygdala	5.8 nTPM
Thalamus	4.8 nTPM
Medulla oblongata	4.2 nTPM
Basal ganglia	3.5 nTPM
Hypothalamus	2.4 nTPM

Cerebellar inhibitory	8.5 nTPM
Medulla oblongata	11.0 nTPM
Pons	10.3 nTPM
Cerebellum	8.5 nTPM
Midbrain	7.2 nTPM
Spinal cord	5.5 nTPM

Cge interneuron	17.3 nTPM
Hypothalamus	24.9 nTPM
Amygdala	19.3 nTPM
Basal ganglia	16.4 nTPM
Midbrain	16.0 nTPM
Cerebral cortex	15.8 nTPM
Hippocampus	15.8 nTPM
Thalamus	13.2 nTPM

Choroid plexus epithelial cell	78.3 nTPM
Basal ganglia	102.3 nTPM
Thalamus	95.9 nTPM
Medulla oblongata	64.9 nTPM
Hippocampus	49.9 nTPM

Committed oligodendrocyte precursor	340.8 nTPM
Hypothalamus	486.8 nTPM
Amygdala	434.7 nTPM
Hippocampus	416.0 nTPM
Cerebral cortex	397.7 nTPM
Midbrain	353.7 nTPM
Spinal cord	349.5 nTPM
Thalamus	325.3 nTPM
Cerebellum	294.9 nTPM
Basal ganglia	272.1 nTPM
Pons	252.3 nTPM
Medulla oblongata	165.2 nTPM

Deep-layer corticothalamic and 6b	15.0 nTPM
Hypothalamus	27.0 nTPM
Amygdala	19.9 nTPM
Basal ganglia	14.9 nTPM
Midbrain	10.0 nTPM
Hippocampus	9.7 nTPM
Cerebral cortex	8.3 nTPM

Deep-layer intratelencephalic	11.6 nTPM
Hypothalamus	16.0 nTPM
Amygdala	12.6 nTPM
Hippocampus	11.7 nTPM
Basal ganglia	9.3 nTPM
Cerebral cortex	8.3 nTPM

Deep-layer near-projecting	15.4 nTPM
Hypothalamus	24.6 nTPM
Basal ganglia	20.1 nTPM
Amygdala	13.4 nTPM
Cerebral cortex	11.5 nTPM
Hippocampus	7.5 nTPM

Eccentric medium spiny neuron	30.2 nTPM
Amygdala	36.7 nTPM
Cerebral cortex	36.0 nTPM
Hypothalamus	34.1 nTPM
Hippocampus	31.9 nTPM
Thalamus	23.0 nTPM
Basal ganglia	19.3 nTPM

Endothelial cell	74.7 nTPM
Basal ganglia	90.4 nTPM
Amygdala	82.7 nTPM
Thalamus	80.2 nTPM
Cerebellum	79.8 nTPM
Hippocampus	78.5 nTPM
Cerebral cortex	75.4 nTPM
Pons	74.9 nTPM
Hypothalamus	73.2 nTPM
Midbrain	69.9 nTPM
Spinal cord	63.9 nTPM
Medulla oblongata	52.3 nTPM

Ependymal cell	60.3 nTPM
Amygdala	104.1 nTPM
Hippocampus	76.3 nTPM
Basal ganglia	64.9 nTPM
Pons	64.8 nTPM
Spinal cord	55.6 nTPM
Hypothalamus	50.9 nTPM
Midbrain	45.1 nTPM
Medulla oblongata	41.9 nTPM
Thalamus	38.9 nTPM