Single cell type - CALD1 - 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.	CALD1
Gene descriptionⁱ Full gene name according to HGNC.	Caldesmon 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	12

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	Smooth muscle cells - 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 (Smooth muscle cells, Sertoli cells, Peritubular cells, Leydig cells, Endometrial stromal 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	Immune cell enriched (neutrophil)
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 single
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 (BJ hTERT+, fHDF/TERT166, U-138 MG)
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

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 (Smooth muscle cells, Sertoli cells, Peritubular cells, Leydig cells, Endometrial stromal 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

CALD1 is part of cluster 48 Smooth muscle cells - ECM organization with confidenceⁱ 1
270 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
TAGLN	Transgelin	0.8137	48
TGFB1I1	Transforming growth factor beta 1 induced transcript 1	0.7707	48
MYL9	Myosin light chain 9	0.7669	48
ACTA2	Actin alpha 2, smooth muscle	0.7655	48
REM1	RRAD and GEM like GTPase 1	0.7640	48
MYLK	Myosin light chain kinase	0.7569	48
GPR20	G protein-coupled receptor 20	0.7397	48
MYH11	Myosin heavy chain 11	0.7319	48
FOXL1	Forkhead box L1	0.7255	48
MRGPRF	MAS related GPR family member F	0.7223	48
CSRP1	Cysteine and glycine rich protein 1	0.7083	48
RASL12	RAS like family 12	0.7068	48
KCNJ8	Potassium inwardly rectifying channel subfamily J member 8	0.7027	48
RERGL	RERG like	0.7017	48
LMOD1	Leiomodin 1	0.6990	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

Adipocytes	400.6 nTPM
Breast	484.9 nTPM
Adipose tissue	316.3 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	17.6 nTPM
Lung	17.6 nTPM

Astrocytes	43.1 nTPM
Brain	43.1 nTPM

B-cells	7.3 nTPM
Kidney	38.1 nTPM
Liver	21.1 nTPM
Breast	10.7 nTPM
Adipose tissue	1.5 nTPM
Stomach	1.4 nTPM
Lymph node	0.7 nTPM
Colon	0.0 nTPM
PBMC	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Basal squamous epithelial cells	164.4 nTPM
Esophagus	164.4 nTPM

Dendritic cells	5.0 nTPM
Breast	14.2 nTPM
Adipose tissue	0.8 nTPM
PBMC	0.0 nTPM

Endothelial cells	432.9 nTPM
Eye	804.3 nTPM
Pancreas	606.1 nTPM
Skeletal muscle	594.1 nTPM
Ovary	530.6 nTPM
Breast	486.9 nTPM
Testis	431.1 nTPM
Lung	427.3 nTPM
Skin	409.4 nTPM
Endometrium	380.4 nTPM
Placenta	347.3 nTPM
Heart muscle	338.0 nTPM
Liver	281.6 nTPM
Prostate	252.5 nTPM
Esophagus	170.3 nTPM

Fibroblasts	886.9 nTPM
Placenta	1707.2 nTPM
Breast	1133.7 nTPM
Adipose tissue	1069.7 nTPM
Esophagus	1017.2 nTPM
Prostate	816.6 nTPM
Stomach	809.3 nTPM
Ovary	805.8 nTPM
Heart muscle	670.3 nTPM
Skeletal muscle	627.5 nTPM
Skin	610.5 nTPM
Lung	488.1 nTPM

Intestinal goblet cells	1.2 nTPM
Colon	2.2 nTPM
Small intestine	0.8 nTPM
Rectum	0.6 nTPM

Macrophages	38.8 nTPM
PBMC	231.9 nTPM
Endometrium	72.4 nTPM
Prostate	58.5 nTPM
Skeletal muscle	54.9 nTPM
Testis	51.2 nTPM
Kidney	34.0 nTPM
Esophagus	33.1 nTPM
Breast	16.8 nTPM
Ovary	10.9 nTPM
Pancreas	7.7 nTPM
Lung	6.2 nTPM
Adipose tissue	3.8 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.2 nTPM
Rectum	0.6 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	4.2 nTPM
Esophagus	12.3 nTPM
Stomach	5.4 nTPM
Adipose tissue	3.3 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Respiratory ciliated cells	11.3 nTPM
Bronchus	12.3 nTPM
Lung	10.2 nTPM

Smooth muscle cells	2549.3 nTPM
Heart muscle	4258.3 nTPM
Prostate	3953.9 nTPM
Skeletal muscle	3209.6 nTPM
Esophagus	2739.8 nTPM
Pancreas	2708.5 nTPM
Breast	2417.6 nTPM
Endometrium	2391.1 nTPM
Adipose tissue	2364.3 nTPM
Ovary	1819.0 nTPM
Skin	1809.6 nTPM
Bronchus	370.2 nTPM

Cholangiocytes	228.8 nTPM
Liver	228.8 nTPM

Collecting duct cells	44.1 nTPM
Kidney	44.1 nTPM

Cytotrophoblasts	202.7 nTPM
Placenta	202.7 nTPM

Distal tubular cells	23.5 nTPM
Kidney	23.5 nTPM

T-cells	27.5 nTPM
Endometrium	90.8 nTPM
Skin	82.9 nTPM
Skeletal muscle	66.4 nTPM
Prostate	52.1 nTPM
Esophagus	45.9 nTPM
Lung	41.0 nTPM
Kidney	30.2 nTPM
Ovary	22.3 nTPM
Breast	15.1 nTPM
Liver	14.9 nTPM
PBMC	2.6 nTPM
Colon	1.0 nTPM
Stomach	1.0 nTPM
Adipose tissue	0.6 nTPM
Lymph node	0.2 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Undifferentiated cells	0.8 nTPM
Colon	1.9 nTPM
Small intestine	0.3 nTPM
Rectum	0.2 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