Single cell type - SCAI - 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.	SCAI
Gene descriptionⁱ Full gene name according to HGNC.	Suppressor of cancer cell invasion
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.	2

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.	Neurons - Neuronal signaling (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 (Excitatory neurons, Inhibitory neurons, Rod photoreceptor 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.	0.58
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.	Low cell type specificity
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.	Not detected in immune cells
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 (Excitatory neurons, Inhibitory neurons, Rod photoreceptor 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: Low cell type specificity

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: Not detected in immune cells
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

SCAI is part of cluster 34 Neurons - Neuronal signaling with confidenceⁱ 1
518 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.
NRG1	Neuregulin 1	0.8712	34
TCERG1L	Transcription elongation regulator 1 like	0.8299	34
CACNG3	Calcium voltage-gated channel auxiliary subunit gamma 3	0.8212	65
STXBP5L	Syntaxin binding protein 5L	0.7939	34
GABRA5	Gamma-aminobutyric acid type A receptor subunit alpha5	0.7930	34
SYT1	Synaptotagmin 1	0.7914	65
C4orf50	Chromosome 4 open reading frame 50	0.7850	34
RGPD6	RANBP2 like and GRIP domain containing 6	0.7798	65
ZNF804B	Zinc finger protein 804B	0.7687	34
PLCB1	Phospholipase C beta 1	0.7587	65
KCNH1	Potassium voltage-gated channel subfamily H member 1	0.7575	34
POU6F2	POU class 6 homeobox 2	0.7542	34
POLN	DNA polymerase nu	0.7506	34
OR9Q1	Olfactory receptor family 9 subfamily Q member 1	0.7502	34
NWD2	NACHT and WD repeat domain containing 2	0.7495	34

IMMUNE CELLS

SCAI is part of cluster 23 B-cells - Immunoglobulins with confidenceⁱ 0.89
208 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.
BTBD18	BTB domain containing 18	1.0000	23
H1-5	H1.5 linker histone, cluster member	1.0000	23
TOMM34	Translocase of outer mitochondrial membrane 34	1.0000	23
PNPLA7	Patatin like phospholipase domain containing 7	0.9762	18
CNNM4	Cyclin and CBS domain divalent metal cation transport mediator 4	0.9762	23
IFT172	Intraflagellar transport 172	0.9524	13
NPIPA9	Nuclear pore complex interacting protein family, member A9	0.9524	23
GNG7	G protein subunit gamma 7	0.9524	23
LRRTM4	Leucine rich repeat transmembrane neuronal 4	0.9524	18
TLR10	Toll like receptor 10	0.9524	23
ALG14	ALG14 UDP-N-acetylglucosaminyltransferase subunit	0.9524	13
PARM1	Prostate androgen-regulated mucin-like protein 1	0.9524	23
IRF4	Interferon regulatory factor 4	0.9524	23
RTN4IP1	Reticulon 4 interacting protein 1	0.9524	13
CCDC32	Coiled-coil domain containing 32	0.9524	23