Single cell type - CACFD1 - 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.	CACFD1
Gene descriptionⁱ Full gene name according to HGNC.	Calcium channel flower domain containing 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Transporters
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	Membrane
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	Intestinal epithelial cells - Unknown function (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 (Distal enterocytes, Gastric mucus-secreting cells, Paneth cells, Hepatocytes)
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 enhanced (basophil)
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 some
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 (T-47d)
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 (Distal enterocytes, Gastric mucus-secreting cells, Paneth cells, Hepatocytes)

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

CACFD1 is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
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
CU639417.1	Histone H2B type F-S-like	0.7237	53
MST1R	Macrophage stimulating 1 receptor	0.6930	53
TRPM4	Transient receptor potential cation channel subfamily M member 4	0.6850	53
ASL	Argininosuccinate lyase	0.6584	53
BATF2	Basic leucine zipper ATF-like transcription factor 2	0.6389	53
INF2	Inverted formin 2	0.6252	53
ARHGEF16	Rho guanine nucleotide exchange factor 16	0.6247	53
E4F1	E4F transcription factor 1	0.6234	53
CAPN8	Calpain 8	0.6211	16
MMP15	Matrix metallopeptidase 15	0.6132	53
FP565260.2	Novel protein	0.6076	53
IL17RE	Interleukin 17 receptor E	0.6038	53
MYO7B	Myosin VIIB	0.6008	45
MICALL2	MICAL like 2	0.5993	53
RASSF7	Ras association domain family member 7	0.5980	53

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	1.7 nTPM
Adipose tissue	2.0 nTPM
Breast	1.4 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	19.6 nTPM
Lung	19.6 nTPM

Astrocytes	3.3 nTPM
Brain	3.3 nTPM

B-cells	5.5 nTPM
Stomach	12.3 nTPM
Spleen	9.3 nTPM
Colon	8.0 nTPM
Breast	5.3 nTPM
Bone marrow	4.9 nTPM
Lymph node	4.6 nTPM
PBMC	4.3 nTPM
Liver	3.7 nTPM
Adipose tissue	3.0 nTPM
Kidney	0.0 nTPM

Dendritic cells	1.0 nTPM
Breast	1.8 nTPM
Adipose tissue	1.2 nTPM
PBMC	0.0 nTPM

Endothelial cells	3.8 nTPM
Liver	11.9 nTPM
Endometrium	6.8 nTPM
Testis	4.7 nTPM
Esophagus	4.7 nTPM
Skin	4.4 nTPM
Ovary	4.2 nTPM
Placenta	4.0 nTPM
Breast	3.5 nTPM
Eye	2.4 nTPM
Heart muscle	2.2 nTPM
Prostate	2.1 nTPM
Skeletal muscle	2.0 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	4.0 nTPM
Placenta	8.0 nTPM
Stomach	6.0 nTPM
Prostate	5.5 nTPM
Skin	4.7 nTPM
Ovary	4.1 nTPM
Breast	3.9 nTPM
Esophagus	3.8 nTPM
Heart muscle	3.2 nTPM
Adipose tissue	2.8 nTPM
Skeletal muscle	2.3 nTPM
Lung	0.0 nTPM

Intestinal goblet cells	43.1 nTPM
Colon	51.4 nTPM
Rectum	39.3 nTPM
Small intestine	38.5 nTPM

Macrophages	2.1 nTPM
Bone marrow	5.0 nTPM
Kidney	3.8 nTPM
Esophagus	3.1 nTPM
Testis	2.9 nTPM
Stomach	2.9 nTPM
Skeletal muscle	2.5 nTPM
Lung	2.4 nTPM
Ovary	2.3 nTPM
Endometrium	1.4 nTPM
Adipose tissue	1.3 nTPM
Prostate	1.2 nTPM
Breast	1.2 nTPM
Spleen	1.0 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM

Paneth cells	53.2 nTPM
Colon	82.3 nTPM
Small intestine	45.0 nTPM
Rectum	32.3 nTPM

Plasma cells	3.9 nTPM
Stomach	7.4 nTPM
Esophagus	6.1 nTPM
Bone marrow	3.3 nTPM
Adipose tissue	1.3 nTPM
Spleen	1.3 nTPM

Respiratory ciliated cells	5.2 nTPM
Bronchus	8.9 nTPM
Lung	1.5 nTPM

Smooth muscle cells	4.4 nTPM
Esophagus	7.8 nTPM
Ovary	6.5 nTPM
Prostate	5.3 nTPM
Pancreas	4.9 nTPM
Endometrium	4.6 nTPM
Adipose tissue	3.9 nTPM
Heart muscle	3.8 nTPM
Breast	3.4 nTPM
Skeletal muscle	3.2 nTPM
Skin	2.8 nTPM
Bronchus	2.0 nTPM

T-cells	1.9 nTPM
Kidney	4.7 nTPM
Prostate	4.7 nTPM
Endometrium	3.4 nTPM
Stomach	3.1 nTPM
Liver	2.9 nTPM
PBMC	2.2 nTPM
Colon	1.9 nTPM
Bone marrow	1.8 nTPM
Breast	1.6 nTPM
Lung	1.5 nTPM
Spleen	1.2 nTPM
Lymph node	1.1 nTPM
Skin	0.9 nTPM
Adipose tissue	0.9 nTPM
Skeletal muscle	0.8 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Cholangiocytes	21.5 nTPM
Liver	21.5 nTPM

Collecting duct cells	20.2 nTPM
Kidney	20.2 nTPM

Cone photoreceptor cells	12.5 nTPM
Eye	12.5 nTPM

Distal enterocytes	75.5 nTPM
Colon	95.6 nTPM
Rectum	55.4 nTPM

Undifferentiated cells	24.5 nTPM
Colon	40.6 nTPM
Rectum	21.1 nTPM
Small intestine	11.8 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