Single cell type - SDC1 - 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.	SDC1
Gene descriptionⁱ Full gene name according to HGNC.	Syndecan 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes CD markers Metabolic proteins Plasma proteins 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.	Secreted, Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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.	Squamous epithelial cells - Keratinization (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 (Hepatocytes, Suprabasal keratinocytes, Syncytiotrophoblasts, Squamous epithelial cells, Cholangiocytes, Alveolar cells type 1)
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.	0.61
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, Thalamic excitatory)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

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 (Hepatocytes, Suprabasal keratinocytes, Syncytiotrophoblasts, Squamous epithelial cells, Cholangiocytes, Alveolar cells type 1)

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, Thalamic excitatory)

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

SDC1 is part of cluster 12 Squamous epithelial cells - Keratinization with confidenceⁱ 1
309 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.
CRYBG2	Crystallin beta-gamma domain containing 2	0.6553	59
NECTIN1	Nectin cell adhesion molecule 1	0.5703	12
NECTIN4	Nectin cell adhesion molecule 4	0.5543	27
EPHX3	Epoxide hydrolase 3	0.5358	59
SQLE	Squalene epoxidase	0.5229	62
FAM83H	Family with sequence similarity 83 member H	0.5227	72
GJB2	Gap junction protein beta 2	0.5224	59
FGFBP1	Fibroblast growth factor binding protein 1	0.5209	12
SDR16C5	Short chain dehydrogenase/reductase family 16C member 5	0.5205	35
ADH7	Alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	0.5193	12
CLCA2	Chloride channel accessory 2	0.5185	12
MAB21L4	Mab-21 like 4	0.5177	59
FAM83G	Family with sequence similarity 83 member G	0.5152	12
FOXE1	Forkhead box E1	0.5122	12
LYPD3	LY6/PLAUR domain containing 3	0.5100	59

IMMUNE CELLS

SDC1 is part of cluster 17 B-cells - Immunoglobulins with confidenceⁱ 1
129 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.
IGLV2-18	Immunoglobulin lambda variable 2-18	1.0000	17
TAS1R3	Taste 1 receptor member 3	1.0000	17
COL4A3	Collagen type IV alpha 3 chain	1.0000	17
PLAAT2	Phospholipase A and acyltransferase 2	1.0000	17
PTPRB	Protein tyrosine phosphatase receptor type B	1.0000	17
BHLHE41	Basic helix-loop-helix family member e41	0.9762	17
SGO1	Shugoshin 1	0.9762	17
IGLL1	Immunoglobulin lambda like polypeptide 1	0.9762	17
CPNE5	Copine 5	0.9762	17
BTN1A1	Butyrophilin subfamily 1 member A1	0.9762	17
EHD3	EH domain containing 3	0.9762	23
DYNC2I2	Dynein 2 intermediate chain 2	0.9762	17
CAV1	Caveolin 1	0.9762	17
SIGLEC6	Sialic acid binding Ig like lectin 6	0.9762	23
COCH	Cochlin	0.9762	17