Single cell type - SDK2 - 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.	SDK2
Gene descriptionⁱ Full gene name according to HGNC.	Sidekick cell adhesion molecule 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.	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.	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 (Extravillous trophoblasts, Excitatory neurons, Late spermatids, Oocytes, Early spermatids, Syncytiotrophoblasts)
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.	0.66
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 (Deep-layer corticothalamic and 6b)
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 (Extravillous trophoblasts, Excitatory neurons, Late spermatids, Oocytes, Early spermatids, Syncytiotrophoblasts)

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 (Deep-layer corticothalamic and 6b)

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

SDK2 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.
KCNF1	Potassium voltage-gated channel modifier subfamily F member 1	0.5944	69
DNAH14	Dynein axonemal heavy chain 14	0.5016	69
KCNG2	Potassium voltage-gated channel modifier subfamily G member 2	0.4930	69
SORCS3	Sortilin related VPS10 domain containing receptor 3	0.4912	34
CHRNB3	Cholinergic receptor nicotinic beta 3 subunit	0.4865	69
CPLX2	Complexin 2	0.4854	71
AFF3	ALF transcription elongation factor 3	0.4809	73
KCNB2	Potassium voltage-gated channel subfamily B member 2	0.4795	69
NRXN1	Neurexin 1	0.4783	34
SEZ6L	Seizure related 6 homolog like	0.4779	34
KCNT2	Potassium sodium-activated channel subfamily T member 2	0.4765	69
NELL1	Neural EGFL like 1	0.4747	34
CDH10	Cadherin 10	0.4686	34
ASXL3	ASXL transcriptional regulator 3	0.4620	69
SCN2A	Sodium voltage-gated channel alpha subunit 2	0.4569	69

IMMUNE CELLS

SDK2 is part of cluster 30 Non-specific - DNA binding with confidenceⁱ 1
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.
MRTO4	MRT4 homolog, ribosome maturation factor	1.0000	30
NSUN4	NOP2/Sun RNA methyltransferase 4	0.9762	30
DDI2	DNA damage inducible 1 homolog 2	0.9762	30
CCDC51	Coiled-coil domain containing 51	0.9762	30
EARS2	Glutamyl-tRNA synthetase 2, mitochondrial	0.9524	30
ARFGEF2	ADP ribosylation factor guanine nucleotide exchange factor 2	0.9524	30
CARMIL1	Capping protein regulator and myosin 1 linker 1	0.9524	30
ATXN2L	Ataxin 2 like	0.9524	30
TMEM192	Transmembrane protein 192	0.9524	30
FAM120C	Family with sequence similarity 120C	0.9524	30
PFDN6	Prefoldin subunit 6	0.9524	30
APEX1	Apurinic/apyrimidinic endodeoxyribonuclease 1	0.9286	30
DHODH	Dihydroorotate dehydrogenase (quinone)	0.9286	30
EIF4G1	Eukaryotic translation initiation factor 4 gamma 1	0.9286	8
LRRC42	Leucine rich repeat containing 42	0.9286	30