Single cell type - H2BC13 - 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.	H2BC13
Gene descriptionⁱ Full gene name according to HGNC.	H2B clustered histone 13
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	Intracellular
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.	Plasma cells - Immunoglobulins & histones (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 (Gastric mucus-secreting cells, Plasma cells, Pancreatic endocrine cells)
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.	0.92
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.	Not detected
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 (neutrophil)
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 (Gastric mucus-secreting cells, Plasma cells, Pancreatic endocrine cells)

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: Not detected

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 (neutrophil)
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

H2BC13 is part of cluster 61 Plasma cells - Immunoglobulins & histones with confidenceⁱ 0.97
169 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.
H2AC17	H2A clustered histone 17	0.8940	61
H2AC4	H2A clustered histone 4	0.8935	61
H2BC17	H2B clustered histone 17	0.8434	61
H3C7	H3 clustered histone 7	0.8285	52
H2BC14	H2B clustered histone 14	0.8232	61
H3C8	H3 clustered histone 8	0.8079	61
H2AC11	H2A clustered histone 11	0.7803	61
H2AC12	H2A clustered histone 12	0.7798	61
H2AC14	H2A clustered histone 14	0.7750	52
H3C2	H3 clustered histone 2	0.7732	61
H2BC3	H2B clustered histone 3	0.7656	61
H2AC13	H2A clustered histone 13	0.7646	61
H4C4	H4 clustered histone 4	0.7520	61
H4C13	H4 clustered histone 13	0.7493	61
H3C12	H3 clustered histone 12	0.7478	61

IMMUNE CELLS

H2BC13 is part of cluster 22 Eosinophils - Transcription with confidenceⁱ 0.64
357 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.
ZNF518B	Zinc finger protein 518B	0.9762	22
FAM78A	Family with sequence similarity 78 member A	0.9762	25
SH3BP5L	SH3 binding domain protein 5 like	0.9524	19
PIK3C3	Phosphatidylinositol 3-kinase catalytic subunit type 3	0.9524	25
ARHGEF18	Rho/Rac guanine nucleotide exchange factor 18	0.9524	22
CCDC9	Coiled-coil domain containing 9	0.9524	19
S1PR4	Sphingosine-1-phosphate receptor 4	0.9524	19
TRAPPC14	Trafficking protein particle complex subunit 14	0.9286	21
C1orf131	Chromosome 1 open reading frame 131	0.9286	22
SSH2	Slingshot protein phosphatase 2	0.9286	19
ZNF574	Zinc finger protein 574	0.9286	22
SIGLEC8	Sialic acid binding Ig like lectin 8	0.9048	22
PIK3R2	Phosphoinositide-3-kinase regulatory subunit 2	0.9048	22
NUDCD3	NudC domain containing 3	0.9048	22
GATA1	GATA binding protein 1	0.9048	22