Single cell type - FAM3A - 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.	FAM3A
Gene descriptionⁱ Full gene name according to HGNC.	FAM3 metabolism regulating signaling molecule A
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,Membrane,Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	9

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	Enterocytes - Digestion (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 (Proximal enterocytes)
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	Cell line enhanced (EFO-21)
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
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 (Proximal enterocytes)

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

FAM3A is part of cluster 45 Enterocytes - Digestion with confidenceⁱ 1
268 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
GATA5	GATA binding protein 5	0.6519	45
RBBP8NL	RBBP8 N-terminal like	0.6500	45
AQP12A	Aquaporin 12A	0.6447	45
SULT1C3	Sulfotransferase family 1C member 3	0.6085	27
KAZALD1	Kazal type serine peptidase inhibitor domain 1	0.6052	27
STBD1	Starch binding domain 1	0.6045	45
B4GALNT2	Beta-1,4-N-acetyl-galactosaminyltransferase 2	0.5906	27
PHGR1	Proline, histidine and glycine rich 1	0.5883	45
HID1	HID1 domain containing	0.5791	27
P2RY4	Pyrimidinergic receptor P2Y4	0.5725	27
TBX10	T-box transcription factor 10	0.5707	27
URAD	Ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase	0.5610	45
DQX1	DEAQ-box RNA dependent ATPase 1	0.5493	45
ZP2	Zona pellucida glycoprotein 2	0.5461	45
HECTD3	HECT domain E3 ubiquitin protein ligase 3	0.5391	45

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	23.5 nTPM
Breast	27.4 nTPM
Adipose tissue	19.6 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	16.7 nTPM
Lung	16.7 nTPM

Astrocytes	13.1 nTPM
Brain	13.1 nTPM

B-cells	16.9 nTPM
Breast	28.1 nTPM
Bone marrow	24.5 nTPM
Colon	22.3 nTPM
Lymph node	20.6 nTPM
Spleen	17.6 nTPM
Liver	16.9 nTPM
Stomach	14.5 nTPM
PBMC	11.5 nTPM
Adipose tissue	8.5 nTPM
Kidney	4.8 nTPM

Dendritic cells	19.3 nTPM
Breast	23.6 nTPM
PBMC	20.0 nTPM
Adipose tissue	14.2 nTPM

Endothelial cells	18.3 nTPM
Eye	25.1 nTPM
Breast	24.8 nTPM
Placenta	23.3 nTPM
Testis	23.1 nTPM
Liver	22.0 nTPM
Skin	21.3 nTPM
Esophagus	21.0 nTPM
Ovary	20.4 nTPM
Skeletal muscle	16.9 nTPM
Prostate	14.0 nTPM
Endometrium	12.2 nTPM
Pancreas	11.6 nTPM
Heart muscle	10.7 nTPM
Lung	9.3 nTPM

Fibroblasts	28.4 nTPM
Placenta	44.5 nTPM
Esophagus	40.4 nTPM
Adipose tissue	39.8 nTPM
Breast	37.8 nTPM
Prostate	31.1 nTPM
Ovary	29.5 nTPM
Skeletal muscle	27.8 nTPM
Skin	23.5 nTPM
Stomach	19.3 nTPM
Heart muscle	11.6 nTPM
Lung	6.7 nTPM

Intestinal goblet cells	58.9 nTPM
Small intestine	76.3 nTPM
Colon	51.4 nTPM
Rectum	48.8 nTPM

Macrophages	18.0 nTPM
Pancreas	30.7 nTPM
Ovary	28.8 nTPM
Breast	22.0 nTPM
Stomach	20.5 nTPM
Testis	19.2 nTPM
Esophagus	18.9 nTPM
Kidney	17.5 nTPM
Bone marrow	16.3 nTPM
Spleen	15.6 nTPM
Skeletal muscle	15.0 nTPM
Adipose tissue	14.7 nTPM
Lung	14.6 nTPM
Prostate	13.8 nTPM
PBMC	13.6 nTPM
Endometrium	8.5 nTPM

Paneth cells	57.5 nTPM
Colon	72.5 nTPM
Small intestine	52.6 nTPM
Rectum	47.4 nTPM

Plasma cells	32.5 nTPM
Esophagus	49.4 nTPM
Stomach	47.1 nTPM
Bone marrow	28.0 nTPM
Spleen	24.3 nTPM
Adipose tissue	13.6 nTPM

Respiratory ciliated cells	12.7 nTPM
Bronchus	16.8 nTPM
Lung	8.7 nTPM

Smooth muscle cells	24.5 nTPM
Breast	39.8 nTPM
Esophagus	35.7 nTPM
Pancreas	32.1 nTPM
Ovary	30.1 nTPM
Adipose tissue	28.8 nTPM
Skeletal muscle	24.1 nTPM
Prostate	21.6 nTPM
Skin	16.7 nTPM
Heart muscle	15.8 nTPM
Endometrium	13.2 nTPM
Bronchus	11.3 nTPM

T-cells	19.3 nTPM
Lymph node	28.8 nTPM
Liver	27.0 nTPM
Breast	27.0 nTPM
Ovary	24.5 nTPM
Stomach	23.2 nTPM
Spleen	22.7 nTPM
Bone marrow	22.2 nTPM
Kidney	22.0 nTPM
Colon	20.9 nTPM
PBMC	20.5 nTPM
Skin	19.3 nTPM
Prostate	14.2 nTPM
Lung	13.6 nTPM
Skeletal muscle	12.9 nTPM
Adipose tissue	12.2 nTPM
Endometrium	10.1 nTPM
Esophagus	6.6 nTPM

Basal prostatic cells	23.4 nTPM
Prostate	23.4 nTPM

Basal respiratory cells	29.2 nTPM
Bronchus	29.2 nTPM

Basal squamous epithelial cells	22.8 nTPM
Esophagus	22.8 nTPM

Cholangiocytes	22.8 nTPM
Liver	22.8 nTPM

Undifferentiated cells	39.7 nTPM
Rectum	42.7 nTPM
Small intestine	38.8 nTPM
Colon	37.8 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