Single cell type - SALL2 - 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.	SALL2
Gene descriptionⁱ Full gene name according to HGNC.	Spalt like transcription factor 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes Transcription factors
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.	Bipolar cells - Visual perception (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 (Cone photoreceptor cells, Oocytes, Astrocytes, Horizontal cells, Muller glia 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.	0.75
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 (Ependymal 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.	Immune cell enhanced (naive CD8 T-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 (Cone photoreceptor cells, Oocytes, Astrocytes, Horizontal cells, Muller glia 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 (Ependymal 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: Immune cell enhanced (naive CD8 T-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

SALL2 is part of cluster 25 Bipolar cells - Visual perception with confidenceⁱ 1
152 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.
RAB3A	RAB3A, member RAS oncogene family	0.6645	25
PRRT1	Proline rich transmembrane protein 1	0.6554	25
MAGEE2	MAGE family member E2	0.6440	71
ATP1B2	ATPase Na+/K+ transporting subunit beta 2	0.6312	25
ASIC4	Acid sensing ion channel subunit family member 4	0.6201	25
CIART	Circadian associated repressor of transcription	0.6124	10
TCEAL5	Transcription elongation factor A like 5	0.6122	25
DTX3	Deltex E3 ubiquitin ligase 3	0.5839	6
BEX1	Brain expressed X-linked 1	0.5792	25
TCEAL6	Transcription elongation factor A like 6	0.5728	25
B4GAT1	Beta-1,4-glucuronyltransferase 1	0.5701	24
ECEL1	Endothelin converting enzyme like 1	0.5693	25
TCEAL2	Transcription elongation factor A like 2	0.5552	6
ATP6V1G2	ATPase H+ transporting V1 subunit G2	0.5541	25
USP11	Ubiquitin specific peptidase 11	0.5471	25

IMMUNE CELLS

SALL2 is part of cluster 30 Non-specific - DNA binding with confidenceⁱ 0.99
263 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.
ATP10A	ATPase phospholipid transporting 10A (putative)	1.0000	30
CCDC92	Coiled-coil domain containing 92	0.9762	5
SUPT3H	SPT3 homolog, SAGA and STAGA complex component	0.9762	3
B4GAT1	Beta-1,4-glucuronyltransferase 1	0.9762	3
GAL3ST4	Galactose-3-O-sulfotransferase 4	0.9524	30
FHL1	Four and a half LIM domains 1	0.9524	5
HOXB2	Homeobox B2	0.9286	11
PPT2	Palmitoyl-protein thioesterase 2	0.9286	30
ASAH2B	N-acylsphingosine amidohydrolase 2B	0.9286	5
NT5C1B	5'-nucleotidase, cytosolic IB	0.9286	30
TSPYL2	TSPY like 2	0.9286	30
RBIS	Ribosomal biogenesis factor	0.9286	30
PTPRM	Protein tyrosine phosphatase receptor type M	0.9286	30
DDIT4	DNA damage inducible transcript 4	0.9286	5
GRAMD2B	GRAM domain containing 2B	0.9286	30