Single cell type - SPARCL1 - 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.	SPARCL1
Gene descriptionⁱ Full gene name according to HGNC.	SPARC like 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-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.	10

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	Adipocytes & Endothelial cells - Angiogenesis (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, Adipocytes, Smooth muscle cells, Peritubular cells, Skeletal myocytes, Endothelial 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	Not detected in immune cells
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	Not detected
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	Group enriched (AF22, SuSa, U-266/70)
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
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, Adipocytes, Smooth muscle cells, Peritubular cells, Skeletal myocytes, Endothelial 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

SPARCL1 is part of cluster 14 Adipocytes & Endothelial cells - Angiogenesis with confidenceⁱ 1
354 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
F8	Coagulation factor VIII	0.7136	14
EPAS1	Endothelial PAS domain protein 1	0.7090	14
TMEM204	Transmembrane protein 204	0.6914	14
OR51E1	Olfactory receptor family 51 subfamily E member 1	0.6864	48
DAZ2	Deleted in azoospermia 2	0.6733	43
FZD4	Frizzled class receptor 4	0.6678	14
TACC1	Transforming acidic coiled-coil containing protein 1	0.6640	14
FMO2	Flavin containing dimethylaniline monoxygenase 2	0.6627	14
SHISA3	Shisa family member 3	0.6601	43
TIMP3	TIMP metallopeptidase inhibitor 3	0.6506	48
ADAMTS1	ADAM metallopeptidase with thrombospondin type 1 motif 1	0.6450	48
SMIM10	Small integral membrane protein 10	0.6432	48
ITGA1	Integrin subunit alpha 1	0.6378	14
TPO	Thyroid peroxidase	0.6256	14
NRP1	Neuropilin 1	0.6201	14

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	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	56.4 nTPM
Lung	56.4 nTPM

Astrocytes	1155.7 nTPM
Brain	1155.7 nTPM

B-cells	6.2 nTPM
Breast	28.1 nTPM
Kidney	14.3 nTPM
Liver	13.4 nTPM
Lymph node	4.6 nTPM
Stomach	1.4 nTPM
Colon	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Basal keratinocytes	46.3 nTPM
Skin	46.3 nTPM

Adipocytes	4430.9 nTPM
Adipose tissue	5474.8 nTPM
Breast	3387.0 nTPM

Dendritic cells	8.6 nTPM
Breast	24.8 nTPM
Adipose tissue	0.8 nTPM
PBMC	0.0 nTPM

Endothelial cells	2372.1 nTPM
Testis	5614.6 nTPM
Heart muscle	4900.1 nTPM
Skeletal muscle	4698.0 nTPM
Esophagus	3136.2 nTPM
Prostate	2840.2 nTPM
Breast	2548.5 nTPM
Ovary	1977.4 nTPM
Eye	1818.1 nTPM
Endometrium	1573.6 nTPM
Skin	1422.7 nTPM
Lung	1297.5 nTPM
Placenta	970.8 nTPM
Liver	279.8 nTPM
Pancreas	131.3 nTPM

Fibroblasts	1413.1 nTPM
Heart muscle	5249.9 nTPM
Esophagus	3112.7 nTPM
Prostate	2020.9 nTPM
Stomach	1851.7 nTPM
Skeletal muscle	1700.1 nTPM
Lung	641.2 nTPM
Breast	348.2 nTPM
Adipose tissue	239.1 nTPM
Ovary	215.7 nTPM
Skin	149.7 nTPM
Placenta	14.7 nTPM

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

Macrophages	31.6 nTPM
Skeletal muscle	176.3 nTPM
Esophagus	92.8 nTPM
Testis	66.9 nTPM
Prostate	44.7 nTPM
Endometrium	37.6 nTPM
Breast	24.0 nTPM
Lung	18.3 nTPM
Stomach	5.9 nTPM
Kidney	5.3 nTPM
Adipose tissue	2.2 nTPM
Ovary	0.1 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

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

Plasma cells	25.2 nTPM
Esophagus	117.0 nTPM
Stomach	7.6 nTPM
Adipose tissue	1.3 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Respiratory ciliated cells	7.4 nTPM
Lung	14.6 nTPM
Bronchus	0.1 nTPM

Smooth muscle cells	2781.9 nTPM
Heart muscle	13206.1 nTPM
Skeletal muscle	4293.6 nTPM
Prostate	3773.3 nTPM
Adipose tissue	3148.1 nTPM
Esophagus	2671.6 nTPM
Breast	2169.5 nTPM
Skin	732.3 nTPM
Endometrium	438.4 nTPM
Ovary	163.2 nTPM
Pancreas	4.5 nTPM
Bronchus	0.0 nTPM

Cholangiocytes	4.3 nTPM
Liver	4.3 nTPM

Collecting duct cells	7.3 nTPM
Kidney	7.3 nTPM

Cone photoreceptor cells	2.1 nTPM
Eye	2.1 nTPM

Distal tubular cells	13.7 nTPM
Kidney	13.7 nTPM

T-cells	26.9 nTPM
Skeletal muscle	200.2 nTPM
Endometrium	69.1 nTPM
Skin	55.3 nTPM
Lung	53.2 nTPM
Esophagus	32.8 nTPM
Breast	25.9 nTPM
Kidney	5.5 nTPM
Prostate	4.7 nTPM
Lymph node	3.5 nTPM
Liver	2.9 nTPM
Ovary	2.2 nTPM
Stomach	1.4 nTPM
Adipose tissue	0.5 nTPM
Colon	0.0 nTPM
PBMC	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	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