Single cell type - SPARC - 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.	SPARC
Gene descriptionⁱ Full gene name according to HGNC.	Secreted protein acidic and cysteine rich
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Disease related genes Human disease related genes Plasma proteins
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,Secreted
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	Fibroblasts - ECM organization (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 (Sertoli cells, Smooth muscle cells, Endometrial stromal cells, Peritubular cells, Fibroblasts, Theca cells, Endothelial cells, Adipocytes)
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	Group enriched (neutrophil, basophil, classical monocyte)
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 (ASC diff, BJ, fHDF/TERT166, WM-115)
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 many
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
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. Read more	Protein predicted to be secreted

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 (Sertoli cells, Smooth muscle cells, Endometrial stromal cells, Peritubular cells, Fibroblasts, Theca cells, Endothelial cells, Adipocytes)

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

SPARC is part of cluster 33 Fibroblasts - ECM organization with confidenceⁱ 1
171 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
EFEMP2	EGF containing fibulin extracellular matrix protein 2	0.8181	33
PCOLCE	Procollagen C-endopeptidase enhancer	0.8019	10
COL1A1	Collagen type I alpha 1 chain	0.7590	33
COL5A1	Collagen type V alpha 1 chain	0.7483	33
COL3A1	Collagen type III alpha 1 chain	0.7423	33
FKBP10	FKBP prolyl isomerase 10	0.7379	33
RCN3	Reticulocalbin 3	0.7152	33
CTHRC1	Collagen triple helix repeat containing 1	0.6993	33
LOXL2	Lysyl oxidase like 2	0.6948	33
LGALS1	Galectin 1	0.6833	10
EMILIN1	Elastin microfibril interfacer 1	0.6723	33
VASN	Vasorin	0.6719	48
PELO	Pelota mRNA surveillance and ribosome rescue factor	0.6673	33
MMP23B	Matrix metallopeptidase 23B	0.6637	33
TGFB1I1	Transforming growth factor beta 1 induced transcript 1	0.6557	48

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

Alveolar cells type 1	83.3 nTPM
Lung	83.3 nTPM

Alveolar cells type 2	27.5 nTPM
Lung	27.5 nTPM

Astrocytes	7.2 nTPM
Brain	7.2 nTPM

B-cells	6.8 nTPM
Liver	23.9 nTPM
Kidney	23.8 nTPM
Breast	10.7 nTPM
PBMC	7.1 nTPM
Stomach	1.4 nTPM
Lymph node	0.8 nTPM
Colon	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Basal keratinocytes	164.8 nTPM
Skin	164.8 nTPM

Adipocytes	737.1 nTPM
Adipose tissue	745.4 nTPM
Breast	728.9 nTPM

Dendritic cells	2.8 nTPM
Breast	8.1 nTPM
Adipose tissue	0.3 nTPM
PBMC	0.0 nTPM

Endothelial cells	781.9 nTPM
Ovary	2623.5 nTPM
Placenta	1619.4 nTPM
Endometrium	1144.9 nTPM
Testis	945.5 nTPM
Pancreas	702.6 nTPM
Prostate	643.8 nTPM
Breast	556.8 nTPM
Skin	522.0 nTPM
Eye	495.2 nTPM
Heart muscle	439.0 nTPM
Esophagus	432.6 nTPM
Lung	355.6 nTPM
Skeletal muscle	349.3 nTPM
Liver	116.5 nTPM

Fibroblasts	1032.1 nTPM
Placenta	3452.4 nTPM
Skin	1468.4 nTPM
Ovary	1051.3 nTPM
Adipose tissue	1011.7 nTPM
Skeletal muscle	940.5 nTPM
Stomach	914.7 nTPM
Esophagus	583.8 nTPM
Lung	572.0 nTPM
Breast	557.5 nTPM
Prostate	434.7 nTPM
Heart muscle	365.6 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Macrophages	92.0 nTPM
PBMC	1050.3 nTPM
Endometrium	78.6 nTPM
Skeletal muscle	61.1 nTPM
Lung	38.6 nTPM
Testis	37.2 nTPM
Kidney	19.6 nTPM
Esophagus	18.9 nTPM
Prostate	18.4 nTPM
Ovary	16.8 nTPM
Breast	15.4 nTPM
Pancreas	15.3 nTPM
Adipose tissue	5.9 nTPM
Spleen	3.1 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

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

Plasma cells	4.1 nTPM
Esophagus	12.3 nTPM
Stomach	3.8 nTPM
Adipose tissue	2.7 nTPM
Spleen	1.6 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	7.8 nTPM
Lung	10.2 nTPM
Bronchus	5.3 nTPM

Smooth muscle cells	1527.3 nTPM
Bronchus	4312.5 nTPM
Pancreas	3234.1 nTPM
Endometrium	1703.8 nTPM
Adipose tissue	1425.0 nTPM
Heart muscle	1311.3 nTPM
Skeletal muscle	1275.8 nTPM
Ovary	955.5 nTPM
Skin	716.3 nTPM
Esophagus	641.9 nTPM
Prostate	614.8 nTPM
Breast	608.8 nTPM

Cholangiocytes	5.7 nTPM
Liver	5.7 nTPM

Collecting duct cells	16.5 nTPM
Kidney	16.5 nTPM

Cone photoreceptor cells	2.1 nTPM
Eye	2.1 nTPM

Cytotrophoblasts	115.4 nTPM
Placenta	115.4 nTPM

T-cells	21.1 nTPM
Skin	120.7 nTPM
Endometrium	106.1 nTPM
Skeletal muscle	62.2 nTPM
Lung	30.4 nTPM
Liver	14.2 nTPM
Breast	9.6 nTPM
PBMC	8.1 nTPM
Kidney	5.5 nTPM
Stomach	1.0 nTPM
Lymph node	0.7 nTPM
Adipose tissue	0.3 nTPM
Bone marrow	0.3 nTPM
Spleen	0.2 nTPM
Colon	0.0 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 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