Single cell type - SCOC - 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.	SCOC
Gene descriptionⁱ Full gene name according to HGNC.	Short coiled-coil protein
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.	9

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	Early spermatids - Spermatogenesis (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 (Early spermatids, Distal tubular cells, Proximal tubular 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	Low immune cell specificity
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 all
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	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. Read more	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 (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 (Early spermatids, Distal tubular cells, Proximal tubular 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

SCOC is part of cluster 29 Early spermatids - Spermatogenesis with confidenceⁱ 1
337 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
C2orf74	Chromosome 2 open reading frame 74	0.7177	29
CXXC5	CXXC finger protein 5	0.6717	29
LMO1	LIM domain only 1	0.6537	29
NDUFB6	NADH:ubiquinone oxidoreductase subunit B6	0.6237	23
SLC35A5	Solute carrier family 35 member A5	0.6033	29
ZNF610	Zinc finger protein 610	0.5972	29
RNF14	Ring finger protein 14	0.5968	23
FANCF	FA complementation group F	0.5915	23
CCDC121	Coiled-coil domain containing 121	0.5855	29
PKHD1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	0.5769	29
HINT3	Histidine triad nucleotide binding protein 3	0.5744	23
FAM186A	Family with sequence similarity 186 member A	0.5667	29
SVIP	Small VCP interacting protein	0.5648	29
RNF148	Ring finger protein 148	0.5621	29
PDILT	Protein disulfide isomerase like, testis expressed	0.5542	29

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	63.2 nTPM
Breast	70.8 nTPM
Adipose tissue	55.5 nTPM

Alveolar cells type 1	48.1 nTPM
Lung	48.1 nTPM

Alveolar cells type 2	47.2 nTPM
Lung	47.2 nTPM

Astrocytes	15.3 nTPM
Brain	15.3 nTPM

B-cells	34.4 nTPM
Kidney	52.4 nTPM
Spleen	51.5 nTPM
Bone marrow	41.7 nTPM
Stomach	38.1 nTPM
PBMC	34.3 nTPM
Lymph node	30.1 nTPM
Liver	27.8 nTPM
Breast	24.1 nTPM
Colon	23.9 nTPM
Adipose tissue	19.5 nTPM

Dendritic cells	31.3 nTPM
Breast	36.8 nTPM
PBMC	35.8 nTPM
Adipose tissue	21.2 nTPM

Endothelial cells	54.4 nTPM
Testis	72.0 nTPM
Pancreas	69.5 nTPM
Esophagus	65.8 nTPM
Placenta	63.6 nTPM
Breast	63.6 nTPM
Skin	63.0 nTPM
Heart muscle	58.7 nTPM
Endometrium	52.0 nTPM
Prostate	48.4 nTPM
Skeletal muscle	46.7 nTPM
Ovary	46.3 nTPM
Liver	44.9 nTPM
Eye	39.7 nTPM
Lung	28.1 nTPM

Fibroblasts	58.3 nTPM
Heart muscle	84.1 nTPM
Placenta	76.9 nTPM
Breast	72.4 nTPM
Stomach	65.3 nTPM
Esophagus	62.1 nTPM
Adipose tissue	62.0 nTPM
Skin	57.0 nTPM
Prostate	56.7 nTPM
Ovary	42.4 nTPM
Skeletal muscle	40.6 nTPM
Lung	22.4 nTPM

Intestinal goblet cells	42.7 nTPM
Rectum	48.3 nTPM
Colon	42.9 nTPM
Small intestine	37.0 nTPM

Macrophages	34.5 nTPM
Kidney	66.6 nTPM
Pancreas	51.0 nTPM
Lung	45.9 nTPM
Testis	43.0 nTPM
PBMC	40.9 nTPM
Breast	36.9 nTPM
Ovary	36.5 nTPM
Prostate	35.5 nTPM
Bone marrow	31.2 nTPM
Endometrium	29.0 nTPM
Esophagus	26.8 nTPM
Spleen	23.9 nTPM
Adipose tissue	17.9 nTPM
Skeletal muscle	17.6 nTPM
Stomach	14.7 nTPM

Paneth cells	37.0 nTPM
Rectum	48.0 nTPM
Colon	32.9 nTPM
Small intestine	30.0 nTPM

Plasma cells	30.8 nTPM
Spleen	41.9 nTPM
Stomach	39.2 nTPM
Esophagus	36.9 nTPM
Bone marrow	24.7 nTPM
Adipose tissue	11.6 nTPM

Respiratory ciliated cells	54.9 nTPM
Lung	59.8 nTPM
Bronchus	50.0 nTPM

Smooth muscle cells	64.5 nTPM
Heart muscle	102.1 nTPM
Pancreas	86.3 nTPM
Esophagus	82.2 nTPM
Breast	81.3 nTPM
Prostate	61.8 nTPM
Skin	57.1 nTPM
Adipose tissue	56.2 nTPM
Ovary	55.1 nTPM
Skeletal muscle	45.4 nTPM
Endometrium	45.0 nTPM
Bronchus	36.6 nTPM

T-cells	36.3 nTPM
Kidney	63.6 nTPM
Prostate	61.6 nTPM
Spleen	45.1 nTPM
PBMC	44.7 nTPM
Bone marrow	43.1 nTPM
Lymph node	41.2 nTPM
Stomach	37.5 nTPM
Breast	37.3 nTPM
Esophagus	32.8 nTPM
Ovary	31.1 nTPM
Liver	29.7 nTPM
Skin	29.5 nTPM
Lung	28.8 nTPM
Colon	26.6 nTPM
Endometrium	25.9 nTPM
Skeletal muscle	20.4 nTPM
Adipose tissue	18.1 nTPM

Basal keratinocytes	61.1 nTPM
Skin	61.1 nTPM

Basal prostatic cells	69.7 nTPM
Prostate	69.7 nTPM

Basal respiratory cells	74.1 nTPM
Bronchus	74.1 nTPM

Basal squamous epithelial cells	78.6 nTPM
Esophagus	78.6 nTPM

Undifferentiated cells	46.1 nTPM
Colon	55.0 nTPM
Small intestine	41.9 nTPM
Rectum	41.4 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