Single cell type - BOK - 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.	BOK
Gene descriptionⁱ Full gene name according to HGNC.	BCL2 family apoptosis regulator BOK
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma proteins 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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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.	Alveolar cells - Lung 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.	Cell type enhanced (Hepatocytes, Alveolar cells type 1, Oligodendrocytes, Alveolar cells type 2)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.59
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Group enriched (Oligodendrocyte, Committed oligodendrocyte precursor)
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.	Immune cell enhanced (gdT-cell)
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

Single cell type

Cell type enrichment

Single nuclei - Brain

Immune cells

Expression clustering

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Hepatocytes, Alveolar cells type 1, Oligodendrocytes, Alveolar cells type 2)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Group enriched (Oligodendrocyte, Committed oligodendrocyte precursor)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Immune cell enhanced (gdT-cell)
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

BOK is part of cluster 72 Alveolar cells - Lung function with confidenceⁱ 1
121 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CYB5A	Cytochrome b5 type A	0.5738	43
HYAL1	Hyaluronidase 1	0.5266	56
FMO5	Flavin containing dimethylaniline monoxygenase 5	0.5158	43
NDST1	N-deacetylase and N-sulfotransferase 1	0.5136	17
FAM83H	Family with sequence similarity 83 member H	0.5007	72
CERS2	Ceramide synthase 2	0.4928	62
MYO1B	Myosin IB	0.4874	48
AGER	Advanced glycosylation end-product specific receptor	0.4834	72
C1orf116	Chromosome 1 open reading frame 116	0.4753	72
IGFBP1	Insulin like growth factor binding protein 1	0.4747	43
EMP2	Epithelial membrane protein 2	0.4702	72
CLDN14	Claudin 14	0.4680	45
NIBAN2	Niban apoptosis regulator 2	0.4664	59
CCND1	Cyclin D1	0.4643	45
FAH	Fumarylacetoacetate hydrolase	0.4642	56

IMMUNE CELLS

BOK is part of cluster 24 Non-specific - Transcription with confidenceⁱ 0.88
516 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CCL25	C-C motif chemokine ligand 25	1.0000	24
ENSG00000258989	Novel protein	1.0000	24
TRGV1	T cell receptor gamma variable 1 (non-functional)	1.0000	24
VIT	Vitrin	1.0000	24
ACER1	Alkaline ceramidase 1	1.0000	24
S100B	S100 calcium binding protein B	1.0000	24
ZFYVE9	Zinc finger FYVE-type containing 9	1.0000	24
IRF6	Interferon regulatory factor 6	1.0000	24
CRTAM	Cytotoxic and regulatory T cell molecule	1.0000	24
TMEM255A	Transmembrane protein 255A	0.9762	24
NFIX	Nuclear factor I X	0.9762	24
MATN2	Matrilin 2	0.9762	1
LGR6	Leucine rich repeat containing G protein-coupled receptor 6	0.9762	1
C12orf29	Chromosome 12 open reading frame 29	0.9762	24
CLK4	CDC like kinase 4	0.9762	24