Single cell type - ITGA6 - 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.	ITGA6
Gene descriptionⁱ Full gene name according to HGNC.	Integrin subunit alpha 6
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes CD markers Disease related genes Human disease related genes Plasma proteins Potential drug targets 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	Intracellular,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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	Epithelial cell types - Mixed 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 (Adipocytes, Urothelial cells, Basal keratinocytes)
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 (eosinophil)
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 (BJ, HaCaT, HBEC3-KT, hTCEpi, hTERT-HME1)
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 (Adipocytes, Urothelial cells, Basal keratinocytes)

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

ITGA6 is part of cluster 22 Epithelial cell types - Mixed function with confidenceⁱ 1
298 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
EFNB1	Ephrin B1	0.5672	40
FAM110C	Family with sequence similarity 110 member C	0.5499	22
PPARG	Peroxisome proliferator activated receptor gamma	0.5466	40
EFNB2	Ephrin B2	0.5296	53
HELZ2	Helicase with zinc finger 2	0.5268	40
CMTM8	CKLF like MARVEL transmembrane domain containing 8	0.5259	40
SLC14A1	Solute carrier family 14 member 1 (Kidd blood group)	0.5250	22
SLC35F2	Solute carrier family 35 member F2	0.5227	22
FAM83B	Family with sequence similarity 83 member B	0.5192	22
GJB3	Gap junction protein beta 3	0.5091	22
BCAR3	BCAR3 adaptor protein, NSP family member	0.4992	22
TNFRSF10A	TNF receptor superfamily member 10a	0.4966	44
NOSTRIN	Nitric oxide synthase trafficking	0.4939	14
SOWAHB	Sosondowah ankyrin repeat domain family member B	0.4918	22
SOX7	SRY-box transcription factor 7	0.4904	14

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

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	19.5 nTPM
Lung	19.5 nTPM

Astrocytes	88.5 nTPM
Brain	88.5 nTPM

B-cells	8.8 nTPM
Breast	36.0 nTPM
Liver	18.0 nTPM
Kidney	9.5 nTPM
Colon	6.4 nTPM
Stomach	5.9 nTPM
Adipose tissue	3.5 nTPM
Lymph node	3.4 nTPM
Spleen	2.4 nTPM
Bone marrow	1.7 nTPM
PBMC	1.4 nTPM

Basal prostatic cells	236.4 nTPM
Prostate	236.4 nTPM

Adipocytes	327.2 nTPM
Adipose tissue	405.2 nTPM
Breast	249.3 nTPM

Dendritic cells	14.4 nTPM
Adipose tissue	23.3 nTPM
Breast	20.0 nTPM
PBMC	0.0 nTPM

Endothelial cells	196.0 nTPM
Heart muscle	409.3 nTPM
Ovary	346.1 nTPM
Skeletal muscle	329.2 nTPM
Esophagus	306.3 nTPM
Endometrium	243.6 nTPM
Breast	217.8 nTPM
Skin	215.4 nTPM
Eye	168.3 nTPM
Lung	156.0 nTPM
Testis	141.0 nTPM
Prostate	105.5 nTPM
Placenta	62.0 nTPM
Pancreas	38.6 nTPM
Liver	5.5 nTPM

Fibroblasts	20.8 nTPM
Lung	81.5 nTPM
Ovary	35.3 nTPM
Stomach	29.7 nTPM
Heart muscle	21.1 nTPM
Prostate	21.1 nTPM
Skin	15.1 nTPM
Breast	8.1 nTPM
Placenta	6.5 nTPM
Skeletal muscle	5.7 nTPM
Esophagus	4.5 nTPM
Adipose tissue	0.7 nTPM

Intestinal goblet cells	128.8 nTPM
Colon	179.4 nTPM
Rectum	113.4 nTPM
Small intestine	93.6 nTPM

Macrophages	10.0 nTPM
PBMC	27.3 nTPM
Prostate	24.1 nTPM
Endometrium	20.1 nTPM
Ovary	12.4 nTPM
Kidney	12.0 nTPM
Lung	10.6 nTPM
Esophagus	9.4 nTPM
Breast	8.9 nTPM
Stomach	8.8 nTPM
Skeletal muscle	6.3 nTPM
Adipose tissue	3.6 nTPM
Testis	2.9 nTPM
Spleen	2.1 nTPM
Bone marrow	1.2 nTPM
Pancreas	0.0 nTPM

Paneth cells	104.2 nTPM
Colon	207.5 nTPM
Rectum	71.2 nTPM
Small intestine	33.8 nTPM

Plasma cells	109.0 nTPM
Esophagus	190.9 nTPM
Stomach	142.2 nTPM
Spleen	112.5 nTPM
Bone marrow	62.6 nTPM
Adipose tissue	36.7 nTPM

Respiratory ciliated cells	9.2 nTPM
Bronchus	14.1 nTPM
Lung	4.4 nTPM

Smooth muscle cells	18.4 nTPM
Ovary	77.6 nTPM
Heart muscle	38.0 nTPM
Prostate	23.1 nTPM
Endometrium	15.2 nTPM
Skin	12.9 nTPM
Breast	12.5 nTPM
Bronchus	9.5 nTPM
Skeletal muscle	7.7 nTPM
Pancreas	2.9 nTPM
Esophagus	1.5 nTPM
Adipose tissue	1.2 nTPM

Cholangiocytes	22.8 nTPM
Liver	22.8 nTPM

Collecting duct cells	27.6 nTPM
Kidney	27.6 nTPM

Cone photoreceptor cells	56.3 nTPM
Eye	56.3 nTPM

Cytotrophoblasts	103.8 nTPM
Placenta	103.8 nTPM

T-cells	30.1 nTPM
Lymph node	78.3 nTPM
Bone marrow	47.5 nTPM
Spleen	45.9 nTPM
Skeletal muscle	43.5 nTPM
Adipose tissue	41.2 nTPM
PBMC	39.8 nTPM
Esophagus	39.3 nTPM
Prostate	28.4 nTPM
Endometrium	27.2 nTPM
Breast	22.3 nTPM
Skin	21.2 nTPM
Lung	18.2 nTPM
Liver	16.3 nTPM
Stomach	11.6 nTPM
Ovary	11.1 nTPM
Kidney	10.9 nTPM
Colon	8.1 nTPM

Undifferentiated cells	146.3 nTPM
Colon	217.7 nTPM
Small intestine	124.5 nTPM
Rectum	96.9 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