Single cell type - VPS13C - 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.	VPS13C
Gene descriptionⁱ Full gene name according to HGNC.	Vacuolar protein sorting 13 homolog C
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	5

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	Non-specific - Transcription (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 (Oligodendrocytes, Inhibitory neurons)
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 (Oligodendrocytes, Inhibitory neurons)

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

VPS13C is part of cluster 52 Non-specific - Transcription with confidenceⁱ 0.99
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
KIAA1109	KIAA1109	0.5419	8
TCP11L2	T-complex 11 like 2	0.5416	42
ZC3H7A	Zinc finger CCCH-type containing 7A	0.5107	24
PPIP5K2	Diphosphoinositol pentakisphosphate kinase 2	0.4951	8
ZNF506	Zinc finger protein 506	0.4715	52
SPG11	SPG11 vesicle trafficking associated, spatacsin	0.4693	52
TET2	Tet methylcytosine dioxygenase 2	0.4671	41
AP4E1	Adaptor related protein complex 4 subunit epsilon 1	0.4602	59
MTR	5-methyltetrahydrofolate-homocysteine methyltransferase	0.4513	44
NBN	Nibrin	0.4436	41
USP33	Ubiquitin specific peptidase 33	0.4414	50
DOCK11	Dedicator of cytokinesis 11	0.4380	8
SETX	Senataxin	0.4372	44
ST8SIA4	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	0.4280	41
UBASH3B	Ubiquitin associated and SH3 domain containing B	0.4271	8

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	92.5 nTPM
Adipose tissue	105.6 nTPM
Breast	79.3 nTPM

Alveolar cells type 1	67.3 nTPM
Lung	67.3 nTPM

Alveolar cells type 2	61.6 nTPM
Lung	61.6 nTPM

Astrocytes	161.6 nTPM
Brain	161.6 nTPM

B-cells	108.5 nTPM
Adipose tissue	200.5 nTPM
Lymph node	151.8 nTPM
Bone marrow	148.0 nTPM
Stomach	127.2 nTPM
Breast	120.3 nTPM
Spleen	115.6 nTPM
Colon	84.7 nTPM
PBMC	81.4 nTPM
Liver	31.8 nTPM
Kidney	23.8 nTPM

Dendritic cells	141.1 nTPM
Adipose tissue	181.8 nTPM
PBMC	131.5 nTPM
Breast	110.1 nTPM

Endothelial cells	57.3 nTPM
Heart muscle	134.4 nTPM
Skeletal muscle	92.1 nTPM
Lung	84.2 nTPM
Endometrium	70.4 nTPM
Esophagus	62.8 nTPM
Eye	60.7 nTPM
Breast	60.3 nTPM
Ovary	49.4 nTPM
Skin	46.8 nTPM
Testis	43.5 nTPM
Prostate	34.8 nTPM
Liver	33.9 nTPM
Placenta	20.5 nTPM
Pancreas	7.7 nTPM

Fibroblasts	56.2 nTPM
Adipose tissue	88.5 nTPM
Skeletal muscle	81.9 nTPM
Lung	79.3 nTPM
Heart muscle	75.5 nTPM
Esophagus	65.2 nTPM
Stomach	56.4 nTPM
Breast	53.2 nTPM
Skin	40.1 nTPM
Prostate	34.0 nTPM
Ovary	31.2 nTPM
Placenta	12.8 nTPM

Intestinal goblet cells	29.9 nTPM
Rectum	30.6 nTPM
Colon	30.0 nTPM
Small intestine	29.3 nTPM

Macrophages	107.2 nTPM
Adipose tissue	196.6 nTPM
Bone marrow	170.0 nTPM
Spleen	153.4 nTPM
Skeletal muscle	153.3 nTPM
Stomach	137.7 nTPM
Esophagus	124.3 nTPM
Breast	118.2 nTPM
Ovary	113.0 nTPM
Lung	110.8 nTPM
Endometrium	94.0 nTPM
Kidney	81.6 nTPM
Testis	77.3 nTPM
Prostate	38.9 nTPM
Pancreas	25.5 nTPM
PBMC	13.6 nTPM

Paneth cells	21.0 nTPM
Rectum	27.7 nTPM
Small intestine	18.8 nTPM
Colon	16.5 nTPM

Plasma cells	83.9 nTPM
Adipose tissue	169.7 nTPM
Stomach	94.7 nTPM
Esophagus	74.0 nTPM
Spleen	46.4 nTPM
Bone marrow	34.6 nTPM

Respiratory ciliated cells	113.1 nTPM
Lung	128.2 nTPM
Bronchus	97.9 nTPM

Smooth muscle cells	66.9 nTPM
Heart muscle	208.0 nTPM
Adipose tissue	85.8 nTPM
Skeletal muscle	77.3 nTPM
Breast	70.7 nTPM
Endometrium	64.3 nTPM
Bronchus	51.3 nTPM
Esophagus	51.2 nTPM
Prostate	40.0 nTPM
Ovary	38.7 nTPM
Skin	32.1 nTPM
Pancreas	16.1 nTPM

T-cells	98.8 nTPM
Adipose tissue	196.9 nTPM
Lung	151.8 nTPM
Skeletal muscle	150.2 nTPM
Endometrium	125.7 nTPM
Bone marrow	123.0 nTPM
Spleen	109.7 nTPM
Breast	109.2 nTPM
Stomach	108.9 nTPM
Lymph node	105.8 nTPM
Colon	90.8 nTPM
PBMC	84.9 nTPM
Ovary	73.4 nTPM
Liver	60.0 nTPM
Esophagus	58.9 nTPM
Prostate	47.3 nTPM
Kidney	45.8 nTPM
Skin	36.4 nTPM

Basal keratinocytes	18.6 nTPM
Skin	18.6 nTPM

Basal prostatic cells	32.3 nTPM
Prostate	32.3 nTPM

Basal respiratory cells	33.1 nTPM
Bronchus	33.1 nTPM

Basal squamous epithelial cells	26.7 nTPM
Esophagus	26.7 nTPM

Undifferentiated cells	23.9 nTPM
Rectum	26.8 nTPM
Small intestine	24.1 nTPM
Colon	20.9 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