Single cell type - SEMA6B - 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.	SEMA6B
Gene descriptionⁱ Full gene name according to HGNC.	Semaphorin 6B
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Plasma proteins
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	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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	Alveolar cells - Smell perception (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 (Alveolar cells type 2, Adipocytes, Endothelial cells, Hepatic stellate cells, Macrophages, Excitatory neurons, Inhibitory neurons, granulocytes, Alveolar cells type 1)
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	Not detected in immune cells
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	Not detected
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 (Hep G2, HMC-1, HUVEC TERT2, TIME)
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 (Alveolar cells type 2, Adipocytes, Endothelial cells, Hepatic stellate cells, Macrophages, Excitatory neurons, Inhibitory neurons, granulocytes, Alveolar cells type 1)

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

SEMA6B is part of cluster 11 Alveolar cells - Smell perception with confidenceⁱ 0.9
281 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
MLKL	Mixed lineage kinase domain like pseudokinase	0.6423	11
SCARF1	Scavenger receptor class F member 1	0.5998	14
CD93	CD93 molecule	0.5793	14
ISY1-RAB43	ISY1-RAB43 readthrough	0.5724	11
LY75-CD302	LY75-CD302 readthrough	0.5717	11
XAF1	XIAP associated factor 1	0.5630	14
ICAM4	Intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)	0.5522	11
GGTA1	Glycoprotein alpha-galactosyltransferase 1 (inactive)	0.5507	11
OR5AS1	Olfactory receptor family 5 subfamily AS member 1	0.5497	11
AC093525.2	Novel protein	0.5469	11
RPS10-NUDT3	RPS10-NUDT3 readthrough	0.5460	11
OR6C75	Olfactory receptor family 6 subfamily C member 75	0.5457	11
ICAM1	Intercellular adhesion molecule 1	0.5440	11
ERFE	Erythroferrone	0.5434	11
MAB21L3	Mab-21 like 3	0.5414	11

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

Astrocytes	2.6 nTPM
Brain	2.6 nTPM

B-cells	2.3 nTPM
Colon	12.8 nTPM
Adipose tissue	3.5 nTPM
PBMC	2.8 nTPM
Liver	1.8 nTPM
Breast	1.3 nTPM
Lymph node	0.3 nTPM
Spleen	0.3 nTPM
Kidney	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Basal keratinocytes	4.7 nTPM
Skin	4.7 nTPM

Basal prostatic cells	1.5 nTPM
Prostate	1.5 nTPM

Basal respiratory cells	0.5 nTPM
Bronchus	0.5 nTPM

Dendritic cells	2.3 nTPM
PBMC	4.0 nTPM
Adipose tissue	1.8 nTPM
Breast	1.1 nTPM

Endothelial cells	40.1 nTPM
Ovary	108.2 nTPM
Lung	77.9 nTPM
Skeletal muscle	69.5 nTPM
Endometrium	54.2 nTPM
Prostate	39.7 nTPM
Eye	34.0 nTPM
Placenta	33.5 nTPM
Esophagus	32.1 nTPM
Testis	29.6 nTPM
Pancreas	27.0 nTPM
Breast	21.5 nTPM
Skin	15.4 nTPM
Liver	11.9 nTPM
Heart muscle	6.8 nTPM

Fibroblasts	8.2 nTPM
Lung	49.2 nTPM
Stomach	19.3 nTPM
Skin	6.7 nTPM
Placenta	5.8 nTPM
Adipose tissue	3.5 nTPM
Skeletal muscle	2.5 nTPM
Breast	1.4 nTPM
Prostate	1.0 nTPM
Heart muscle	0.4 nTPM
Esophagus	0.4 nTPM
Ovary	0.2 nTPM

Intestinal goblet cells	0.1 nTPM
Rectum	0.3 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Macrophages	35.2 nTPM
Prostate	130.6 nTPM
Pancreas	102.0 nTPM
Lung	73.0 nTPM
Endometrium	49.9 nTPM
Adipose tissue	42.8 nTPM
Skeletal muscle	31.3 nTPM
Stomach	29.4 nTPM
Esophagus	15.8 nTPM
Ovary	12.8 nTPM
Kidney	11.4 nTPM
Breast	11.3 nTPM
Spleen	9.3 nTPM
Bone marrow	7.5 nTPM
Testis	1.7 nTPM
PBMC	0.0 nTPM

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

Plasma cells	1.1 nTPM
Adipose tissue	5.2 nTPM
Stomach	0.5 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Respiratory ciliated cells	17.7 nTPM
Lung	35.0 nTPM
Bronchus	0.4 nTPM

Smooth muscle cells	1.8 nTPM
Skeletal muscle	4.4 nTPM
Skin	3.5 nTPM
Prostate	2.5 nTPM
Adipose tissue	2.5 nTPM
Endometrium	2.3 nTPM
Breast	2.3 nTPM
Bronchus	1.0 nTPM
Heart muscle	0.8 nTPM
Ovary	0.8 nTPM
Pancreas	0.3 nTPM
Esophagus	0.0 nTPM

T-cells	5.4 nTPM
Lung	65.3 nTPM
Prostate	4.7 nTPM
Endometrium	3.8 nTPM
Skin	3.6 nTPM
Kidney	2.7 nTPM
Liver	2.6 nTPM
Breast	2.4 nTPM
PBMC	2.1 nTPM
Skeletal muscle	2.0 nTPM
Adipose tissue	2.0 nTPM
Colon	0.5 nTPM
Bone marrow	0.1 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Cone photoreceptor cells	4.2 nTPM
Eye	4.2 nTPM

Cytotrophoblasts	0.6 nTPM
Placenta	0.6 nTPM

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