Single cell type - THEMIS2 - 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.	THEMIS2
Gene descriptionⁱ Full gene name according to HGNC.	Thymocyte selection associated family member 2
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.	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.	Dendritic cells - Antigen presentation (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 (Monocytes, Dendritic cells, Kupffer cells, Macrophages, NK-cells, Hofbauer 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.	0.76
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.	Cell type enhanced (Central nervous system macrophage, Leukocyte)
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.	Group enriched (neutrophil, non-classical monocyte, intermediate monocyte, classical monocyte, eosinophil, myeloid DC, plasmacytoid DC)
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 (Monocytes, Dendritic cells, Kupffer cells, Macrophages, NK-cells, Hofbauer 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: Cell type enhanced (Central nervous system macrophage, Leukocyte)

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: Group enriched (neutrophil, non-classical monocyte, intermediate monocyte, classical monocyte, eosinophil, myeloid DC, plasmacytoid DC)
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

THEMIS2 is part of cluster 28 Dendritic cells - Antigen presentation with confidenceⁱ 1
245 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.
OR5B21	Olfactory receptor family 5 subfamily B member 21	0.7422	28
CHML	CHM like Rab escort protein	0.7243	28
IRF8	Interferon regulatory factor 8	0.7059	28
ICOSLG	Inducible T cell costimulator ligand	0.6979	28
GPR183	G protein-coupled receptor 183	0.6852	28
ENTPD7	Ectonucleoside triphosphate diphosphohydrolase 7	0.6834	28
PTPN1	Protein tyrosine phosphatase non-receptor type 1	0.6671	28
PLD4	Phospholipase D family member 4	0.6583	28
SH2B3	SH2B adaptor protein 3	0.6576	28
TAMALIN	Trafficking regulator and scaffold protein tamalin	0.6534	28
NOPCHAP1	NOP protein chaperone 1	0.6531	28
IRF7	Interferon regulatory factor 7	0.6435	28
SH3TC1	SH3 domain and tetratricopeptide repeats 1	0.6417	29
EIF2AK4	Eukaryotic translation initiation factor 2 alpha kinase 4	0.6414	28
CLN8	CLN8 transmembrane ER and ERGIC protein	0.6341	28

IMMUNE CELLS

THEMIS2 is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 0.78
501 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.
TMPPE	Transmembrane protein with metallophosphoesterase domain	1.0000	38
DNAJB12	DnaJ heat shock protein family (Hsp40) member B12	1.0000	38
ATP6V1B2	ATPase H+ transporting V1 subunit B2	0.9762	38
PISD	Phosphatidylserine decarboxylase	0.9762	38
PSMB10	Proteasome 20S subunit beta 10	0.9762	38
NHSL2	NHS like 2	0.9762	38
S100A4	S100 calcium binding protein A4	0.9762	38
RASGRP4	RAS guanyl releasing protein 4	0.9762	7
ARPC5	Actin related protein 2/3 complex subunit 5	0.9762	38
PAK1	P21 (RAC1) activated kinase 1	0.9762	7
IMPA2	Inositol monophosphatase 2	0.9762	7
STX10	Syntaxin 10	0.9762	7
FCGRT	Fc gamma receptor and transporter	0.9762	38
DTX2	Deltex E3 ubiquitin ligase 2	0.9762	38
SPG21	SPG21 abhydrolase domain containing, maspardin	0.9762	38