Single cell type - AFF3 - 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.	AFF3
Gene descriptionⁱ Full gene name according to HGNC.	AF4/FMR2 family member 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-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.	18

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	Neurons & Oligodendrocytes - Neuronal signaling (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 (Excitatory neurons, Inhibitory neurons, Oligodendrocyte precursor cells, B-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	Group enriched (naive B-cell, memory B-cell, plasmacytoid DC)
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 many
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 (Daudi, U-698)
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 (Excitatory neurons, Inhibitory neurons, Oligodendrocyte precursor cells, B-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

AFF3 is part of cluster 21 Neurons & Oligodendrocytes - Neuronal signaling with confidenceⁱ 1
589 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
OR2AG2	Olfactory receptor family 2 subfamily AG member 2	0.7009	21
STRBP	Spermatid perinuclear RNA binding protein	0.6962	21
TMEM241	Transmembrane protein 241	0.6892	21
CHSY3	Chondroitin sulfate synthase 3	0.6758	21
BMPER	BMP binding endothelial regulator	0.6730	21
ADAMTSL1	ADAMTS like 1	0.6721	21
OR52N4	Olfactory receptor family 52 subfamily N member 4	0.6715	21
HECTD2	HECT domain E3 ubiquitin protein ligase 2	0.6714	21
HTR1F	5-hydroxytryptamine receptor 1F	0.6700	21
NUTM2F	NUT family member 2F	0.6666	21
GLIS1	GLIS family zinc finger 1	0.6645	21
ADAMTS19	ADAM metallopeptidase with thrombospondin type 1 motif 19	0.6635	21
PTPRR	Protein tyrosine phosphatase receptor type R	0.6585	21
BTNL2	Butyrophilin like 2	0.6484	21
DCLK1	Doublecortin like kinase 1	0.6468	21

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	1.2 nTPM
Breast	1.5 nTPM
Adipose tissue	1.0 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	40.9 nTPM
Lung	40.9 nTPM

Astrocytes	41.8 nTPM
Brain	41.8 nTPM

Basal keratinocytes	1.8 nTPM
Skin	1.8 nTPM

B-cells	154.9 nTPM
Lymph node	266.2 nTPM
Bone marrow	261.6 nTPM
Adipose tissue	249.2 nTPM
Spleen	202.4 nTPM
Stomach	185.3 nTPM
PBMC	137.1 nTPM
Kidney	85.7 nTPM
Colon	84.7 nTPM
Breast	56.2 nTPM
Liver	21.0 nTPM

Dendritic cells	32.8 nTPM
PBMC	87.6 nTPM
Adipose tissue	9.3 nTPM
Breast	1.5 nTPM

Endothelial cells	6.0 nTPM
Endometrium	39.5 nTPM
Placenta	15.9 nTPM
Lung	9.3 nTPM
Eye	5.7 nTPM
Breast	4.6 nTPM
Skin	2.1 nTPM
Liver	1.8 nTPM
Heart muscle	1.7 nTPM
Skeletal muscle	1.7 nTPM
Prostate	1.2 nTPM
Esophagus	0.6 nTPM
Testis	0.3 nTPM
Ovary	0.2 nTPM
Pancreas	0.0 nTPM

Fibroblasts	13.5 nTPM
Adipose tissue	36.9 nTPM
Skeletal muscle	33.6 nTPM
Ovary	23.2 nTPM
Lung	15.7 nTPM
Heart muscle	8.2 nTPM
Breast	8.2 nTPM
Skin	7.9 nTPM
Stomach	6.0 nTPM
Prostate	4.3 nTPM
Esophagus	2.9 nTPM
Placenta	1.8 nTPM

Intestinal goblet cells	0.5 nTPM
Small intestine	1.4 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM

Macrophages	16.5 nTPM
Adipose tissue	63.2 nTPM
Endometrium	33.2 nTPM
Skeletal muscle	28.9 nTPM
Testis	24.4 nTPM
Prostate	19.5 nTPM
PBMC	13.6 nTPM
Spleen	12.5 nTPM
Breast	12.1 nTPM
Esophagus	11.0 nTPM
Bone marrow	10.0 nTPM
Ovary	9.6 nTPM
Kidney	4.6 nTPM
Lung	4.4 nTPM
Pancreas	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.1 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	0.8 nTPM
Adipose tissue	1.9 nTPM
Stomach	1.7 nTPM
Spleen	0.3 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	0.0 nTPM
Lung	0.0 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	8.5 nTPM
Endometrium	27.0 nTPM
Heart muscle	18.2 nTPM
Breast	8.9 nTPM
Adipose tissue	8.7 nTPM
Prostate	7.8 nTPM
Ovary	7.2 nTPM
Skin	7.0 nTPM
Skeletal muscle	6.4 nTPM
Esophagus	1.5 nTPM
Pancreas	0.3 nTPM
Bronchus	0.0 nTPM

Cytotrophoblasts	0.4 nTPM
Placenta	0.4 nTPM

Early spermatids	33.9 nTPM
Testis	33.9 nTPM

Endometrial stromal cells	19.8 nTPM
Endometrium	19.8 nTPM

Excitatory neurons	491.3 nTPM
Brain	491.3 nTPM

T-cells	6.1 nTPM
Lymph node	16.0 nTPM
Endometrium	14.8 nTPM
Esophagus	13.1 nTPM
Lung	10.6 nTPM
Prostate	9.5 nTPM
Spleen	7.1 nTPM
Colon	6.2 nTPM
Skin	5.5 nTPM
PBMC	4.1 nTPM
Liver	3.1 nTPM
Bone marrow	3.0 nTPM
Breast	2.8 nTPM
Stomach	2.7 nTPM
Adipose tissue	2.6 nTPM
Skeletal muscle	1.3 nTPM
Kidney	0.7 nTPM
Ovary	0.0 nTPM

Undifferentiated cells	0.6 nTPM
Small intestine	1.3 nTPM
Colon	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