Single cell type - HAMP - The Human Protein Atlas

HAMP

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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.	HAMP
Gene descriptionⁱ Full gene name according to HGNC.	Hepcidin antimicrobial peptide
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes Potential drug targets Transporters
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.	2

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.	Hepatocytes - Metabolism (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 (Hepatocytes)
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.	0.90
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 enriched (Central nervous system macrophage)
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.	Group enriched (plasmacytoid DC, myeloid DC)
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 (Hepatocytes)

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 enriched (Central nervous system macrophage)

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: Group enriched (plasmacytoid DC, myeloid DC)
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

HAMP is part of cluster 43 Hepatocytes - Metabolism with confidenceⁱ 1
200 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.
SLC22A1	Solute carrier family 22 member 1	0.9703	43
APCS	Amyloid P component, serum	0.9684	43
TAT	Tyrosine aminotransferase	0.9676	43
SPP2	Secreted phosphoprotein 2	0.9642	43
APOH	Apolipoprotein H	0.9638	43
SERPINC1	Serpin family C member 1	0.9636	43
SLC25A47	Solute carrier family 25 member 47	0.9624	43
ALB	Albumin	0.9621	43
MBL2	Mannose binding lectin 2	0.9613	43
BAAT	Bile acid-CoA:amino acid N-acyltransferase	0.9612	43
MAT1A	Methionine adenosyltransferase 1A	0.9600	43
PON1	Paraoxonase 1	0.9583	43
CCL16	C-C motif chemokine ligand 16	0.9581	43
RBP4	Retinol binding protein 4	0.9577	43
HAO1	Hydroxyacid oxidase 1	0.9573	43

Adipocytes	0.8 nTPM
Breast	1.6 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	2.6 nTPM
Lung	2.6 nTPM

Alveolar cells type 2	0.8 nTPM
Lung	0.8 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	5.5 nTPM
Liver	67.6 nTPM
Lymph node	1.1 nTPM
Stomach	0.8 nTPM
Bone marrow	0.7 nTPM
Spleen	0.7 nTPM
Salivary gland	0.4 nTPM
Thymus	0.2 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	0.3 nTPM
Fallopian tube	0.6 nTPM
Endometrium	0.4 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM

Club cells	0.3 nTPM
Prostate	0.8 nTPM
Lung	0.1 nTPM
Bronchus	0.0 nTPM

Endothelial cells	3.4 nTPM
Liver	54.2 nTPM
Pancreas	2.6 nTPM
Lung	1.2 nTPM
Vascular	0.9 nTPM
Skeletal muscle	0.8 nTPM
Skin	0.6 nTPM
Prostate	0.5 nTPM
Ovary	0.5 nTPM
Endometrium	0.3 nTPM
Tongue	0.3 nTPM
Thymus	0.1 nTPM
Fallopian tube	0.1 nTPM
Testis	0.0 nTPM
Heart muscle	0.0 nTPM
Placenta	0.0 nTPM
Esophagus	0.0 nTPM
Salivary gland	0.0 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	0.6 nTPM
Rectum	1.7 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Fibroblasts	2.6 nTPM
Liver	33.2 nTPM
Pancreas	1.3 nTPM
Lung	1.2 nTPM
Placenta	1.0 nTPM
Vascular	1.0 nTPM
Fallopian tube	1.0 nTPM
Breast	0.9 nTPM
Prostate	0.7 nTPM
Skin	0.4 nTPM
Skeletal muscle	0.1 nTPM
Adipose tissue	0.1 nTPM
Esophagus	0.1 nTPM
Salivary gland	0.1 nTPM
Heart muscle	0.0 nTPM
Stomach	0.0 nTPM
Thymus	0.0 nTPM

Granulocytes	104.1 nTPM
Fallopian tube	312.3 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.6 nTPM
Rectum	1.4 nTPM
Small intestine	0.3 nTPM
Colon	0.2 nTPM

Lymphatic endothelial cells	0.2 nTPM
Fallopian tube	0.4 nTPM
Ovary	0.0 nTPM

Macrophages	27.3 nTPM
Prostate	146.3 nTPM
Fallopian tube	102.9 nTPM
Pancreas	74.0 nTPM
Breast	66.2 nTPM
Endometrium	38.7 nTPM
Thymus	20.6 nTPM
Kidney	16.8 nTPM
Esophagus	14.1 nTPM
Salivary gland	10.5 nTPM
Lung	8.3 nTPM
Skeletal muscle	6.4 nTPM
Stomach	5.1 nTPM
Adipose tissue	3.4 nTPM
Testis	1.9 nTPM
Vascular	1.8 nTPM
Bone marrow	1.0 nTPM
Skin	0.0 nTPM
Spleen	0.0 nTPM
Tongue	0.0 nTPM

Paneth cells	0.2 nTPM
Rectum	0.5 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Cholangiocytes	22.9 nTPM
Liver	22.9 nTPM

Plasma cells	4.8 nTPM
Liver	36.6 nTPM
Fallopian tube	1.3 nTPM
Stomach	0.4 nTPM
Thymus	0.1 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Salivary gland	0.0 nTPM

Schwann cells	0.1 nTPM
Adipose tissue	0.4 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	0.1 nTPM
Salivary gland	0.2 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	2.3 nTPM
Liver	34.0 nTPM
Salivary gland	0.8 nTPM
Skeletal muscle	0.5 nTPM
Placenta	0.4 nTPM
Vascular	0.3 nTPM
Breast	0.3 nTPM
Ovary	0.3 nTPM
Endometrium	0.2 nTPM
Adipose tissue	0.2 nTPM
Fallopian tube	0.2 nTPM
Thymus	0.1 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Tongue	0.0 nTPM

T-cells	2.7 nTPM
Liver	47.5 nTPM
Vascular	2.0 nTPM
Endometrium	1.6 nTPM
Skeletal muscle	1.5 nTPM
Breast	1.3 nTPM
Lymph node	1.0 nTPM
Fallopian tube	0.7 nTPM
Prostate	0.4 nTPM
Lung	0.3 nTPM
PBMC	0.2 nTPM
Tongue	0.2 nTPM
Stomach	0.1 nTPM
Thymus	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Salivary gland	0.0 nTPM

Undifferentiated cells	0.2 nTPM
Small intestine	0.4 nTPM
Rectum	0.3 nTPM
Colon	0.0 nTPM

Amygdala excitatory	0.1 nTPM
Amygdala	0.2 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Hypothalamus	0.1 nTPM
Basal ganglia	0.0 nTPM
Thalamus	0.0 nTPM

Astrocyte	0.2 nTPM
Medulla oblongata	0.3 nTPM
Midbrain	0.3 nTPM
Pons	0.3 nTPM
Spinal cord	0.3 nTPM
Thalamus	0.3 nTPM
Basal ganglia	0.2 nTPM
Cerebellum	0.2 nTPM
Hippocampus	0.2 nTPM
Hypothalamus	0.2 nTPM
Amygdala	0.1 nTPM
Cerebral cortex	0.1 nTPM

Bergmann glia	0.0 nTPM
Cerebellum	0.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	28.2 nTPM
Spinal cord	46.5 nTPM
Medulla oblongata	41.6 nTPM
Pons	36.0 nTPM
Cerebral cortex	31.2 nTPM
Hippocampus	27.3 nTPM
Midbrain	24.7 nTPM
Hypothalamus	22.7 nTPM
Cerebellum	21.8 nTPM
Basal ganglia	21.2 nTPM
Thalamus	20.2 nTPM
Amygdala	17.6 nTPM

Cerebellar inhibitory	0.0 nTPM
Cerebellum	0.1 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.1 nTPM
Midbrain	0.2 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hypothalamus	0.1 nTPM
Amygdala	0.0 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Choroid plexus epithelial cell	0.0 nTPM
Medulla oblongata	0.1 nTPM
Basal ganglia	0.0 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.2 nTPM
Cerebellum	1.6 nTPM
Midbrain	0.8 nTPM
Hippocampus	0.3 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Deep-layer corticothalamic and 6b	0.1 nTPM
Cerebral cortex	0.4 nTPM
Basal ganglia	0.2 nTPM
Hippocampus	0.2 nTPM
Amygdala	0.1 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.1 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Hypothalamus	0.0 nTPM

Deep-layer near-projecting	0.1 nTPM
Amygdala	0.2 nTPM
Hypothalamus	0.2 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM

Eccentric medium spiny neuron	0.2 nTPM
Basal ganglia	0.3 nTPM
Cerebral cortex	0.3 nTPM
Amygdala	0.2 nTPM
Hypothalamus	0.2 nTPM
Thalamus	0.2 nTPM
Hippocampus	0.0 nTPM

Endothelial cell	0.1 nTPM
Thalamus	0.6 nTPM
Hippocampus	0.3 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Ependymal cell	0.1 nTPM
Thalamus	0.4 nTPM
Basal ganglia	0.3 nTPM
Medulla oblongata	0.2 nTPM
Hippocampus	0.1 nTPM
Amygdala	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM