Single cell type - DEF6 - 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.	DEF6
Gene descriptionⁱ Full gene name according to HGNC.	DEF6 guanine nucleotide exchange factor
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.	2

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	NK-cells & T-cells - Immune response (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 (Late spermatids, Hofbauer cells, NK-cells, T-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	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 (JURKAT, MOLT-4, NB-4, REH, THP-1, U-937)
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 (Late spermatids, Hofbauer cells, NK-cells, T-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

DEF6 is part of cluster 63 NK-cells & T-cells - Immune response with confidenceⁱ 1
362 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
DENND2D	DENN domain containing 2D	0.7395	63
DENND1C	DENN domain containing 1C	0.6918	63
TMC8	Transmembrane channel like 8	0.6872	63
RASAL3	RAS protein activator like 3	0.6765	63
LCK	LCK proto-oncogene, Src family tyrosine kinase	0.6728	63
SLFN12L	Schlafen family member 12 like	0.6675	63
UBASH3A	Ubiquitin associated and SH3 domain containing A	0.6481	58
IL27RA	Interleukin 27 receptor subunit alpha	0.6393	63
SCML4	Scm polycomb group protein like 4	0.6391	58
CD8B	CD8b molecule	0.6272	63
SYNRG	Synergin gamma	0.6147	63
RGL4	Ral guanine nucleotide dissociation stimulator like 4	0.6132	63
ZAP70	Zeta chain of T cell receptor associated protein kinase 70	0.6101	63
NLRC3	NLR family CARD domain containing 3	0.6090	63
SLAMF6	SLAM family member 6	0.6084	63

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
Breast	3.1 nTPM
Adipose tissue	0.3 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	8.0 nTPM
Lung	8.0 nTPM

Astrocytes	1.3 nTPM
Brain	1.3 nTPM

B-cells	49.2 nTPM
Lymph node	81.6 nTPM
Stomach	72.7 nTPM
Bone marrow	63.0 nTPM
Spleen	59.1 nTPM
Liver	46.1 nTPM
PBMC	42.8 nTPM
Colon	41.5 nTPM
Adipose tissue	33.0 nTPM
Breast	28.1 nTPM
Kidney	23.8 nTPM

Dendritic cells	52.3 nTPM
Adipose tissue	60.8 nTPM
Breast	52.5 nTPM
PBMC	43.8 nTPM

Endothelial cells	3.1 nTPM
Eye	18.6 nTPM
Liver	4.6 nTPM
Placenta	4.6 nTPM
Esophagus	3.7 nTPM
Skin	3.4 nTPM
Breast	2.3 nTPM
Heart muscle	2.1 nTPM
Skeletal muscle	1.4 nTPM
Endometrium	1.1 nTPM
Testis	0.9 nTPM
Prostate	0.7 nTPM
Ovary	0.3 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	2.2 nTPM
Lung	5.6 nTPM
Stomach	4.4 nTPM
Placenta	3.7 nTPM
Ovary	2.2 nTPM
Breast	2.2 nTPM
Heart muscle	1.6 nTPM
Skin	1.4 nTPM
Skeletal muscle	1.0 nTPM
Esophagus	1.0 nTPM
Prostate	0.9 nTPM
Adipose tissue	0.4 nTPM

Intestinal goblet cells	9.9 nTPM
Colon	13.6 nTPM
Rectum	9.1 nTPM
Small intestine	7.1 nTPM

Macrophages	31.7 nTPM
Breast	55.0 nTPM
Pancreas	43.4 nTPM
Testis	42.4 nTPM
Adipose tissue	40.0 nTPM
Stomach	38.1 nTPM
Bone marrow	33.8 nTPM
Esophagus	33.1 nTPM
Endometrium	31.1 nTPM
Spleen	31.1 nTPM
Prostate	31.0 nTPM
Skeletal muscle	28.9 nTPM
Kidney	27.2 nTPM
Ovary	20.5 nTPM
Lung	19.8 nTPM
PBMC	0.0 nTPM

Paneth cells	8.9 nTPM
Rectum	12.2 nTPM
Small intestine	11.3 nTPM
Colon	3.3 nTPM

Plasma cells	57.9 nTPM
Spleen	79.0 nTPM
Bone marrow	67.6 nTPM
Stomach	66.9 nTPM
Adipose tissue	45.2 nTPM
Esophagus	30.7 nTPM

Respiratory ciliated cells	5.8 nTPM
Bronchus	8.8 nTPM
Lung	2.9 nTPM

Smooth muscle cells	1.2 nTPM
Bronchus	3.8 nTPM
Breast	3.6 nTPM
Skin	1.8 nTPM
Pancreas	1.5 nTPM
Prostate	1.3 nTPM
Ovary	1.0 nTPM
Heart muscle	0.5 nTPM
Endometrium	0.3 nTPM
Skeletal muscle	0.2 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

T-cells	78.3 nTPM
Stomach	127.7 nTPM
Bone marrow	127.6 nTPM
Lymph node	110.4 nTPM
Ovary	106.8 nTPM
Spleen	96.8 nTPM
Liver	91.6 nTPM
Kidney	81.4 nTPM
PBMC	81.1 nTPM
Breast	76.7 nTPM
Colon	66.6 nTPM
Adipose tissue	64.7 nTPM
Skin	57.5 nTPM
Skeletal muscle	54.5 nTPM
Esophagus	52.4 nTPM
Prostate	52.1 nTPM
Lung	45.6 nTPM
Endometrium	37.4 nTPM

Basal keratinocytes	11.9 nTPM
Skin	11.9 nTPM

Basal prostatic cells	16.9 nTPM
Prostate	16.9 nTPM

Basal respiratory cells	15.0 nTPM
Bronchus	15.0 nTPM

Cholangiocytes	2.8 nTPM
Liver	2.8 nTPM

Undifferentiated cells	9.1 nTPM
Small intestine	11.7 nTPM
Rectum	9.5 nTPM
Colon	6.0 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