Single cell type - VEGFD - The Human Protein Atlas

VEGFD

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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.	VEGFD
Gene descriptionⁱ Full gene name according to HGNC.	Vascular endothelial growth factor D
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Plasma proteins RAS pathway related proteins
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.	Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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.	Fibroblasts - ECM organization (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 enriched (Fibroblasts)
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.	0.92
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.	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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

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 enriched (Fibroblasts)

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: 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

VEGFD is part of cluster 53 Fibroblasts - ECM organization with confidenceⁱ 1
305 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.
CFD	Complement factor D	0.8709	53
APOD	Apolipoprotein D	0.8675	53
MYOC	Myocilin	0.8635	53
MAP1LC3C	Microtubule associated protein 1 light chain 3 gamma	0.8376	53
OLFML1	Olfactomedin like 1	0.8270	53
SCARA5	Scavenger receptor class A member 5	0.8191	53
KRTAP13-4	Keratin associated protein 13-4	0.8084	53
GSN	Gelsolin	0.8056	53
CXCL12	C-X-C motif chemokine ligand 12	0.8021	53
GSC	Goosecoid homeobox	0.7987	53
DCN	Decorin	0.7986	53
WNT11	Wnt family member 11	0.7912	53
PDGFRL	Platelet derived growth factor receptor like	0.7902	53
GDF10	Growth differentiation factor 10	0.7888	53
COL6A6	Collagen type VI alpha 6 chain	0.7740	53

Adipocytes	1.3 nTPM
Breast	2.3 nTPM
Adipose tissue	0.4 nTPM

Alveolar cells type 1	1.3 nTPM
Lung	1.3 nTPM

Alveolar cells type 2	0.2 nTPM
Lung	0.2 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	0.1 nTPM
Thymus	0.9 nTPM
Salivary gland	0.6 nTPM
Adipose tissue	0.4 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	0.3 nTPM
Lung	0.4 nTPM
Fallopian tube	0.4 nTPM
Endometrium	0.3 nTPM
Bronchus	0.3 nTPM

Club cells	0.1 nTPM
Bronchus	0.1 nTPM
Lung	0.1 nTPM
Prostate	0.0 nTPM

Endothelial cells	0.7 nTPM
Skeletal muscle	2.5 nTPM
Testis	1.8 nTPM
Prostate	1.4 nTPM
Liver	1.3 nTPM
Esophagus	1.3 nTPM
Heart muscle	0.9 nTPM
Vascular	0.7 nTPM
Skin	0.6 nTPM
Thymus	0.5 nTPM
Lung	0.3 nTPM
Tongue	0.3 nTPM
Ovary	0.3 nTPM
Endometrium	0.2 nTPM
Salivary gland	0.2 nTPM
Fallopian tube	0.2 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	65.4 nTPM
Breast	286.1 nTPM
Esophagus	146.6 nTPM
Adipose tissue	144.1 nTPM
Stomach	139.8 nTPM
Salivary gland	82.4 nTPM
Lung	65.7 nTPM
Skeletal muscle	61.7 nTPM
Vascular	38.9 nTPM
Thymus	37.1 nTPM
Heart muscle	17.5 nTPM
Prostate	13.2 nTPM
Fallopian tube	11.2 nTPM
Skin	2.7 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM

Granulocytes	0.2 nTPM
Lung	0.5 nTPM
Fallopian tube	0.2 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Rectum	0.1 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	0.1 nTPM
Fallopian tube	0.2 nTPM
Ovary	0.0 nTPM

Macrophages	0.7 nTPM
Vascular	2.7 nTPM
Skeletal muscle	2.6 nTPM
Esophagus	2.6 nTPM
Bone marrow	2.0 nTPM
Breast	1.6 nTPM
Thymus	0.8 nTPM
Salivary gland	0.3 nTPM
Adipose tissue	0.2 nTPM
Lung	0.2 nTPM
Fallopian tube	0.2 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM
Tongue	0.0 nTPM

Paneth cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	0.6 nTPM
Stomach	1.3 nTPM
Fallopian tube	1.3 nTPM
Thymus	1.1 nTPM
Spleen	0.5 nTPM
Salivary gland	0.4 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Schwann cells	0.3 nTPM
Vascular	1.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	5.4 nTPM
Salivary gland	10.8 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	3.5 nTPM
Tongue	35.0 nTPM
Adipose tissue	10.0 nTPM
Breast	1.8 nTPM
Liver	1.7 nTPM
Esophagus	1.2 nTPM
Lung	1.2 nTPM
Vascular	1.1 nTPM
Skeletal muscle	0.9 nTPM
Thymus	0.9 nTPM
Placenta	0.7 nTPM
Salivary gland	0.4 nTPM
Fallopian tube	0.3 nTPM
Skin	0.2 nTPM
Ovary	0.2 nTPM
Endometrium	0.0 nTPM
Prostate	0.0 nTPM

T-cells	0.1 nTPM
Vascular	1.2 nTPM
Salivary gland	0.7 nTPM
Breast	0.2 nTPM
Stomach	0.1 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Endometrium	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM

Undifferentiated cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Amygdala excitatory	20.9 nTPM
Thalamus	26.3 nTPM
Hypothalamus	22.7 nTPM
Cerebral cortex	21.0 nTPM
Amygdala	18.8 nTPM
Basal ganglia	18.8 nTPM
Hippocampus	17.5 nTPM

Astrocyte	14.0 nTPM
Amygdala	19.9 nTPM
Cerebral cortex	16.6 nTPM
Midbrain	16.4 nTPM
Hypothalamus	15.1 nTPM
Thalamus	14.8 nTPM
Basal ganglia	14.1 nTPM
Hippocampus	13.9 nTPM
Pons	13.1 nTPM
Cerebellum	10.5 nTPM
Medulla oblongata	9.8 nTPM
Spinal cord	9.5 nTPM

Bergmann glia	11.0 nTPM
Medulla oblongata	12.8 nTPM
Cerebellum	11.4 nTPM
Pons	8.6 nTPM

Central nervous system macrophage	1.7 nTPM
Amygdala	2.7 nTPM
Midbrain	2.1 nTPM
Thalamus	2.0 nTPM
Basal ganglia	1.8 nTPM
Cerebral cortex	1.8 nTPM
Cerebellum	1.7 nTPM
Hypothalamus	1.5 nTPM
Medulla oblongata	1.5 nTPM
Hippocampus	1.4 nTPM
Pons	1.4 nTPM
Spinal cord	1.2 nTPM

Cerebellar inhibitory	12.9 nTPM
Spinal cord	19.2 nTPM
Pons	13.6 nTPM
Midbrain	11.5 nTPM
Cerebellum	10.8 nTPM
Medulla oblongata	9.2 nTPM

Cge interneuron	16.3 nTPM
Amygdala	20.2 nTPM
Hypothalamus	19.7 nTPM
Hippocampus	17.7 nTPM
Cerebral cortex	16.3 nTPM
Basal ganglia	14.8 nTPM
Midbrain	12.9 nTPM
Thalamus	12.6 nTPM

Choroid plexus epithelial cell	10.5 nTPM
Basal ganglia	12.6 nTPM
Thalamus	11.0 nTPM
Medulla oblongata	9.9 nTPM
Hippocampus	8.3 nTPM

Committed oligodendrocyte precursor	6.2 nTPM
Thalamus	14.6 nTPM
Hypothalamus	13.0 nTPM
Amygdala	9.0 nTPM
Midbrain	8.4 nTPM
Basal ganglia	8.2 nTPM
Cerebral cortex	5.7 nTPM
Hippocampus	4.4 nTPM
Pons	3.5 nTPM
Medulla oblongata	1.3 nTPM
Cerebellum	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	22.6 nTPM
Hypothalamus	27.8 nTPM
Hippocampus	27.6 nTPM
Amygdala	23.6 nTPM
Cerebral cortex	22.2 nTPM
Midbrain	17.8 nTPM
Basal ganglia	16.9 nTPM

Deep-layer intratelencephalic	22.8 nTPM
Hypothalamus	27.6 nTPM
Amygdala	23.5 nTPM
Cerebral cortex	22.4 nTPM
Basal ganglia	20.3 nTPM
Hippocampus	20.2 nTPM

Deep-layer near-projecting	29.7 nTPM
Hypothalamus	35.5 nTPM
Amygdala	32.7 nTPM
Cerebral cortex	30.3 nTPM
Basal ganglia	25.3 nTPM
Hippocampus	24.7 nTPM

Eccentric medium spiny neuron	20.6 nTPM
Hypothalamus	24.4 nTPM
Amygdala	23.3 nTPM
Cerebral cortex	22.8 nTPM
Basal ganglia	20.0 nTPM
Thalamus	17.6 nTPM
Hippocampus	15.3 nTPM

Endothelial cell	6.1 nTPM
Pons	8.7 nTPM
Spinal cord	8.6 nTPM
Basal ganglia	7.5 nTPM
Thalamus	6.8 nTPM
Amygdala	6.7 nTPM
Cerebellum	6.2 nTPM
Medulla oblongata	6.2 nTPM
Hypothalamus	5.0 nTPM
Hippocampus	4.5 nTPM
Cerebral cortex	3.8 nTPM
Midbrain	2.8 nTPM

Ependymal cell	1.6 nTPM
Amygdala	4.0 nTPM
Basal ganglia	3.2 nTPM
Hypothalamus	2.7 nTPM
Thalamus	1.6 nTPM
Midbrain	1.3 nTPM
Hippocampus	1.2 nTPM
Medulla oblongata	0.4 nTPM
Pons	0.4 nTPM
Spinal cord	0.0 nTPM