Single cell type - AFF4 - 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.	AFF4
Gene descriptionⁱ Full gene name according to HGNC.	AF4/FMR2 family member 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Disease related genes Human disease related genes
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.	4

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	Endometrium - Transcription (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	Low cell type specificity
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	Low cell line specificity
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

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: Low cell type specificity

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

AFF4 is part of cluster 44 Endometrium - Transcription with confidenceⁱ 1
491 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
TBC1D3L	TBC1 domain family member 3L	0.5628	44
ATXN2L	Ataxin 2 like	0.5485	44
ABI2	Abl interactor 2	0.5075	44
ZFC3H1	Zinc finger C3H1-type containing	0.4856	44
ATP6V1FNB	ATP6V1F neighbor	0.4833	44
PAK5	P21 (RAC1) activated kinase 5	0.4817	40
IGF2BP2	Insulin like growth factor 2 mRNA binding protein 2	0.4795	44
ARIH1	Ariadne RBR E3 ubiquitin protein ligase 1	0.4696	7
TRRAP	Transformation/transcription domain associated protein	0.4691	44
SMG1	SMG1 nonsense mediated mRNA decay associated PI3K related kinase	0.4672	44
CLEC20A	C-type lectin domain containing 20A	0.4658	44
RBBP6	RB binding protein 6, ubiquitin ligase	0.4652	7
TEX45	Testis expressed 45	0.4586	44
NUP153	Nucleoporin 153	0.4583	44
NPHS1	NPHS1 adhesion molecule, nephrin	0.4556	44

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	134.3 nTPM
Adipose tissue	203.4 nTPM
Breast	65.2 nTPM

Alveolar cells type 1	80.1 nTPM
Lung	80.1 nTPM

Alveolar cells type 2	43.9 nTPM
Lung	43.9 nTPM

Astrocytes	62.3 nTPM
Brain	62.3 nTPM

B-cells	98.7 nTPM
Lymph node	184.5 nTPM
Stomach	148.1 nTPM
Adipose tissue	138.8 nTPM
Bone marrow	103.0 nTPM
Spleen	101.8 nTPM
Colon	86.3 nTPM
PBMC	72.9 nTPM
Breast	62.8 nTPM
Kidney	52.4 nTPM
Liver	36.4 nTPM

Basal squamous epithelial cells	140.0 nTPM
Esophagus	140.0 nTPM

Dendritic cells	75.9 nTPM
Adipose tissue	107.5 nTPM
PBMC	63.8 nTPM
Breast	56.5 nTPM

Endothelial cells	79.3 nTPM
Endometrium	158.6 nTPM
Prostate	118.1 nTPM
Skeletal muscle	111.0 nTPM
Esophagus	109.4 nTPM
Eye	105.2 nTPM
Skin	78.0 nTPM
Ovary	69.4 nTPM
Breast	63.9 nTPM
Heart muscle	62.9 nTPM
Testis	55.4 nTPM
Liver	55.0 nTPM
Placenta	54.0 nTPM
Lung	46.8 nTPM
Pancreas	23.1 nTPM

Enteroendocrine cells	97.6 nTPM
Colon	103.1 nTPM
Rectum	92.2 nTPM

Fibroblasts	98.0 nTPM
Stomach	173.7 nTPM
Prostate	137.6 nTPM
Adipose tissue	117.9 nTPM
Esophagus	116.5 nTPM
Lung	106.1 nTPM
Skeletal muscle	98.3 nTPM
Skin	93.3 nTPM
Breast	70.7 nTPM
Ovary	65.7 nTPM
Heart muscle	49.8 nTPM
Placenta	48.0 nTPM

Intestinal goblet cells	59.1 nTPM
Colon	83.6 nTPM
Rectum	51.1 nTPM
Small intestine	42.5 nTPM

Macrophages	100.9 nTPM
Adipose tissue	308.3 nTPM
Endometrium	146.9 nTPM
Stomach	137.7 nTPM
Skeletal muscle	126.2 nTPM
Breast	122.6 nTPM
Prostate	119.3 nTPM
Esophagus	114.9 nTPM
Ovary	100.1 nTPM
Spleen	92.3 nTPM
Bone marrow	72.4 nTPM
Lung	55.9 nTPM
Kidney	46.8 nTPM
Testis	44.1 nTPM
Pancreas	25.5 nTPM
PBMC	0.0 nTPM

Paneth cells	65.5 nTPM
Small intestine	71.4 nTPM
Colon	69.2 nTPM
Rectum	55.9 nTPM

Plasma cells	93.0 nTPM
Stomach	131.9 nTPM
Adipose tissue	127.8 nTPM
Esophagus	117.0 nTPM
Spleen	63.7 nTPM
Bone marrow	24.7 nTPM

Respiratory ciliated cells	53.2 nTPM
Bronchus	54.0 nTPM
Lung	52.5 nTPM

Cholangiocytes	57.2 nTPM
Liver	57.2 nTPM

Collecting duct cells	58.8 nTPM
Kidney	58.8 nTPM

Cone photoreceptor cells	158.4 nTPM
Eye	158.4 nTPM

Distal enterocytes	69.9 nTPM
Colon	79.2 nTPM
Rectum	60.5 nTPM

Smooth muscle cells	103.8 nTPM
Endometrium	170.0 nTPM
Skeletal muscle	135.2 nTPM
Ovary	126.0 nTPM
Prostate	124.7 nTPM
Adipose tissue	118.0 nTPM
Esophagus	114.7 nTPM
Bronchus	99.5 nTPM
Skin	88.3 nTPM
Breast	64.4 nTPM
Heart muscle	61.7 nTPM
Pancreas	39.3 nTPM

T-cells	68.9 nTPM
Endometrium	117.9 nTPM
Lymph node	117.8 nTPM
Adipose tissue	99.6 nTPM
Skeletal muscle	86.9 nTPM
Esophagus	85.2 nTPM
Spleen	79.7 nTPM
Stomach	77.9 nTPM
Breast	66.1 nTPM
Prostate	61.6 nTPM
Skin	58.0 nTPM
Bone marrow	56.3 nTPM
Colon	55.6 nTPM
Liver	54.1 nTPM
PBMC	48.0 nTPM
Lung	38.0 nTPM
Kidney	34.9 nTPM
Ovary	33.3 nTPM

Undifferentiated cells	47.2 nTPM
Colon	57.2 nTPM
Rectum	48.1 nTPM
Small intestine	36.2 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