Cell type atlas - SRM - The Human Protein Atlas

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SRM

SUMMARY

TISSUE

CELL TYPE

PATHOLOGY

BRAIN

BLOOD

CELL

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.	SRM
Gene descriptionⁱ Full gene name according to HGNC.	Spermidine synthase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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.	4

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
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 (Extravillous trophoblasts)
Blood 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	Low cell type specificity
Blood 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.	Low cell line specificity
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.	Detected in all
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 (NX) 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 (Extravillous trophoblasts)

SINGLE CELL TISSUESⁱ Single cell RNA in cell types from tissue are shown separately for each analyzed tissue. For easier navigation across tissues, use the grey browser on the left side of the window. Barchart shows pTPM levels in each 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 Colon
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ RNA expression data (NX) of tissue culture cell lines.The analyzed cell lines are divided into 16 color-coded groups according to the organ they were obtained from. Detailed information about a specific cell line is revealed by hovering over the corresponding bar in the chart. The chart is clickable and redirects to more Cell Atlas data. Read more
Organ Expression Alphabetical

Alveolar cells type 1	0 NX
Lung	0 NX

Alveolar cells type 2	3 NX
Lung	3 NX

B-cells	57 NX
Liver	188 NX
Kidney	58 NX
Colon	57 NX

Basal glandular cells	64 NX
Prostate	64 NX

Basal keratinocytes	84 NX
Skin	84 NX

Bipolar cells	28 NX
Eye	28 NX

Cardiomyocytes	26 NX
Heart muscle	26 NX

Cholangiocytes	31 NX
Liver	31 NX

Ciliated cells	3 NX
Lung	3 NX

Club cells	1 NX
Lung	1 NX

Collecting duct cells	28 NX
Kidney	28 NX

Cone photoreceptor cells	20 NX
Eye	20 NX

Cytotrophoblasts	63 NX
Placenta	63 NX

Distal tubular cells	65 NX
Kidney	65 NX

Ductal cells	20 NX
Pancreas	20 NX

Early spermatids	3 NX
Testis	3 NX

Endothelial cells	47 NX
Prostate	132 NX
Skin	61 NX
Placenta	48 NX
Pancreas	47 NX
Liver	47 NX
Eye	43 NX
Testis	21 NX
Heart muscle	19 NX
Lung	6 NX

Enterocytes	5 NX
Colon	7 NX
Rectum	5 NX
Small intestine	3 NX

Erythroid cells	23 NX
Liver	23 NX

Exocrine glandular cells	37 NX
Pancreas	37 NX

Extravillous trophoblasts	175 NX
Placenta	175 NX

Fibroblasts	66 NX
Prostate	132 NX
Skin	82 NX
Placenta	71 NX
Lung	22 NX
Heart muscle	16 NX

Glandular cells	61 NX
Prostate	61 NX

Granulocytes	28 NX
Colon	55 NX
Lung	0 NX

Hepatocytes	48 NX
Liver	48 NX

Hofbauer cells	85 NX
Placenta	85 NX

Horizontal cells	29 NX
Eye	29 NX

Intestinal endocrine cells	26 NX
Colon	34 NX
Rectum	19 NX

Ito cells	36 NX
Liver	36 NX

Kupffer cells	22 NX
Liver	22 NX

Late spermatids	11 NX
Testis	11 NX

Leydig cells	66 NX
Testis	66 NX

Macrophages	35 NX
Kidney	73 NX
Prostate	61 NX
Pancreas	42 NX
Skin	35 NX
Testis	24 NX
Lung	5 NX

Melanocytes	64 NX
Skin	64 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	8 NX
Pancreas	8 NX

Mucus-secreting cells	27 NX
Colon	60 NX
Rectum	22 NX
Small intestine	18 NX

Muller glia cells	28 NX
Eye	28 NX

Pancreatic endocrine cells	26 NX
Pancreas	26 NX

Paneth cells	7 NX
Rectum	17 NX
Small intestine	7 NX
Colon	6 NX

Peritubular cells	50 NX
Testis	50 NX

Proximal tubular cells	69 NX
Kidney	69 NX

Rod photoreceptor cells	12 NX
Eye	12 NX

Sertoli cells	0 NX
Testis	0 NX

Smooth muscle cells	50 NX
Pancreas	154 NX
Prostate	89 NX
Skin	46 NX
Heart muscle	17 NX

Spermatocytes	13 NX
Testis	13 NX

Spermatogonia	74 NX
Testis	74 NX

Suprabasal keratinocytes	99 NX
Skin	99 NX

Syncytiotrophoblasts	30 NX
Placenta	30 NX

T-cells	24 NX
Kidney	66 NX
Colon	46 NX
Skin	42 NX
Prostate	39 NX
Liver	11 NX
Lung	7 NX

Undifferentiated cells	27 NX
Colon	76 NX
Rectum	26 NX
Small intestine	21 NX

Urothelial cells	92 NX
Prostate	92 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.