Single cell type - AMT - The Human Protein Atlas

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.	AMT
Gene descriptionⁱ Full gene name according to HGNC.	Aminomethyltransferase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic proteins Plasma proteins Potential drug targets
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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	15

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. Read more	Intestinal epithelial cells - Unknown function (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. Read more	Cell type enhanced (Hepatocytes, Proximal enterocytes, Undifferentiated cells)
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. Read more	Immune cell enhanced (NK-cell)
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Cell line enhanced (BEWO, Hep G2, NTERA-2, SH-SY5Y, SuSa)
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in some
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Cell type enhanced (Hepatocytes, Proximal enterocytes, Undifferentiated cells)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

AMT is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
611 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
SLC28A2	Solute carrier family 28 member 2	0.7012	53
SEMA4G	Semaphorin 4G	0.6537	53
ISX	Intestine specific homeobox	0.6221	53
LGALS4	Galectin 4	0.5995	53
NOX1	NADPH oxidase 1	0.5993	53
CDX2	Caudal type homeobox 2	0.5977	53
B3GNT7	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	0.5939	53
NEU4	Neuraminidase 4	0.5904	53
MAMDC4	MAM domain containing 4	0.5776	53
PRAC1	PRAC1 small nuclear protein	0.5752	53
PPP1R1B	Protein phosphatase 1 regulatory inhibitor subunit 1B	0.5671	53
NXPE4	Neurexophilin and PC-esterase domain family member 4	0.5661	53
QTRT1	Queuine tRNA-ribosyltransferase catalytic subunit 1	0.5540	53
TNFRSF11A	TNF receptor superfamily member 11a	0.5454	53
PIGR	Polymeric immunoglobulin receptor	0.5417	53

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	1.2 nTPM
Breast	1.8 nTPM
Adipose tissue	0.7 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	9.2 nTPM
Lung	9.2 nTPM

Astrocytes	11.4 nTPM
Brain	11.4 nTPM

B-cells	3.6 nTPM
Kidney	9.5 nTPM
Colon	4.8 nTPM
PBMC	4.3 nTPM
Breast	4.0 nTPM
Liver	3.7 nTPM
Stomach	3.7 nTPM
Spleen	2.1 nTPM
Lymph node	1.7 nTPM
Bone marrow	1.7 nTPM
Adipose tissue	0.5 nTPM

Dendritic cells	1.4 nTPM
Breast	2.5 nTPM
Adipose tissue	1.5 nTPM
PBMC	0.0 nTPM

Endothelial cells	3.2 nTPM
Heart muscle	8.0 nTPM
Testis	7.4 nTPM
Placenta	5.7 nTPM
Liver	5.5 nTPM
Skeletal muscle	4.3 nTPM
Lung	3.1 nTPM
Skin	2.6 nTPM
Eye	2.4 nTPM
Breast	2.1 nTPM
Prostate	1.1 nTPM
Esophagus	1.0 nTPM
Endometrium	0.8 nTPM
Ovary	0.8 nTPM
Pancreas	0.0 nTPM

Fibroblasts	4.5 nTPM
Heart muscle	16.1 nTPM
Placenta	6.2 nTPM
Esophagus	6.0 nTPM
Skin	4.7 nTPM
Skeletal muscle	4.5 nTPM
Breast	3.2 nTPM
Prostate	3.1 nTPM
Lung	2.2 nTPM
Stomach	1.5 nTPM
Ovary	1.4 nTPM
Adipose tissue	0.5 nTPM

Intestinal goblet cells	18.4 nTPM
Rectum	22.7 nTPM
Small intestine	20.2 nTPM
Colon	12.1 nTPM

Macrophages	2.6 nTPM
Kidney	10.6 nTPM
Lung	7.3 nTPM
Testis	4.0 nTPM
Bone marrow	3.7 nTPM
Breast	3.7 nTPM
Skeletal muscle	3.0 nTPM
Prostate	2.2 nTPM
Spleen	2.1 nTPM
Esophagus	1.6 nTPM
Adipose tissue	0.6 nTPM
Ovary	0.3 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Endometrium	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	18.9 nTPM
Rectum	31.8 nTPM
Small intestine	15.0 nTPM
Colon	9.9 nTPM

Plasma cells	1.1 nTPM
Adipose tissue	1.9 nTPM
Bone marrow	1.7 nTPM
Stomach	1.5 nTPM
Spleen	0.6 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	6.6 nTPM
Lung	7.3 nTPM
Bronchus	6.0 nTPM

Smooth muscle cells	3.1 nTPM
Skin	8.0 nTPM
Skeletal muscle	5.8 nTPM
Heart muscle	4.7 nTPM
Prostate	4.3 nTPM
Bronchus	2.8 nTPM
Breast	2.8 nTPM
Esophagus	1.5 nTPM
Adipose tissue	1.4 nTPM
Endometrium	1.0 nTPM
Pancreas	0.7 nTPM
Ovary	0.6 nTPM

T-cells	3.8 nTPM
Kidney	17.1 nTPM
Liver	7.4 nTPM
Breast	6.5 nTPM
Colon	6.2 nTPM
Lung	6.1 nTPM
Prostate	4.7 nTPM
Skeletal muscle	3.0 nTPM
PBMC	2.7 nTPM
Bone marrow	2.6 nTPM
Endometrium	2.5 nTPM
Spleen	2.0 nTPM
Skin	1.4 nTPM
Lymph node	1.2 nTPM
Stomach	1.0 nTPM
Adipose tissue	0.7 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Cholangiocytes	14.3 nTPM
Liver	14.3 nTPM

Cone photoreceptor cells	20.9 nTPM
Eye	20.9 nTPM

Cytotrophoblasts	25.6 nTPM
Placenta	25.6 nTPM

Distal enterocytes	13.8 nTPM
Colon	14.5 nTPM
Rectum	13.0 nTPM

Undifferentiated cells	31.6 nTPM
Small intestine	36.3 nTPM
Rectum	34.1 nTPM
Colon	24.5 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC