Single cell type - SLC1A1 - 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.	SLC1A1
Gene descriptionⁱ Full gene name according to HGNC.	Solute carrier family 1 member 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes Metabolic proteins Potential drug targets 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.	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.	Glandular & Luminal cells - Unknown 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 (Oligodendrocyte precursor cells, Glandular and luminal cells, Proximal enterocytes, Alveolar cells type 1, Microglial cells, Hepatocytes, Inhibitory neurons, Excitatory neurons)
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.	0.74
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 (Endothelial cell)
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 (Oligodendrocyte precursor cells, Glandular and luminal cells, Proximal enterocytes, Alveolar cells type 1, Microglial cells, Hepatocytes, Inhibitory neurons, Excitatory neurons)

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 (Endothelial cell)

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

SLC1A1 is part of cluster 37 Glandular & Luminal cells - Unknown function with confidenceⁱ 1
334 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.
C2CD4A	C2 calcium dependent domain containing 4A	0.6622	37
RIMKLB	Ribosomal modification protein rimK like family member B	0.6572	37
PAEP	Progestagen associated endometrial protein	0.6532	37
HAP1	Huntingtin associated protein 1	0.6522	37
PCCA	Propionyl-CoA carboxylase subunit alpha	0.6212	37
PAX8	Paired box 8	0.6166	37
ACSL5	Acyl-CoA synthetase long chain family member 5	0.6083	37
S100G	S100 calcium binding protein G	0.6053	22
POU5F1	POU class 5 homeobox 1	0.6022	37
USP43	Ubiquitin specific peptidase 43	0.5973	37
OLIG3	Oligodendrocyte transcription factor 3	0.5887	37
LRATD2	LRAT domain containing 2	0.5858	37
GABRQ	Gamma-aminobutyric acid type A receptor subunit theta	0.5843	37
TXNDC16	Thioredoxin domain containing 16	0.5776	37
HMGCR	3-hydroxy-3-methylglutaryl-CoA reductase	0.5714	37

IMMUNE CELLS

SLC1A1 is part of cluster 9 T-regs - Cell cycle regulation with confidenceⁱ 1
166 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.
HSPA8	Heat shock protein family A (Hsp70) member 8	1.0000	9
JAKMIP1	Janus kinase and microtubule interacting protein 1	1.0000	9
CCNA2	Cyclin A2	1.0000	9
LRIG1	Leucine rich repeats and immunoglobulin like domains 1	1.0000	9
SLC14A1	Solute carrier family 14 member 1 (Kidd blood group)	1.0000	9
TGFB1I1	Transforming growth factor beta 1 induced transcript 1	1.0000	9
CEP55	Centrosomal protein 55	1.0000	9
TOP2A	DNA topoisomerase II alpha	1.0000	9
GINS2	GINS complex subunit 2	1.0000	9
IKZF4	IKAROS family zinc finger 4	1.0000	9
MAD1L1	Mitotic arrest deficient 1 like 1	1.0000	9
NEIL3	Nei like DNA glycosylase 3	1.0000	9
RHOXF1	Rhox homeobox family member 1	1.0000	9
RAD54L	RAD54 like	1.0000	9
LMCD1	LIM and cysteine rich domains 1	1.0000	9