Single cell type - SEMA5A - 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.	SEMA5A
Gene descriptionⁱ Full gene name according to HGNC.	Semaphorin 5A
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Human disease related genes
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, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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.	Oligodendrocyte precursor - 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 enriched (Oligodendrocyte precursor 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.	0.70
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 (Committed oligodendrocyte precursor, Oligodendrocyte precursor cell, Hippocampal dentate gyrus)
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 enriched (plasmacytoid DC)
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 enriched (Oligodendrocyte precursor 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 (Committed oligodendrocyte precursor, Oligodendrocyte precursor cell, Hippocampal dentate gyrus)

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 enriched (plasmacytoid DC)
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

SEMA5A is part of cluster 76 Oligodendrocyte precursor - Unknown function with confidenceⁱ 1
210 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.
LHFPL3	LHFPL tetraspan subfamily member 3	0.8718	76
PCDH15	Protocadherin related 15	0.8549	76
PTPRZ1	Protein tyrosine phosphatase receptor type Z1	0.8425	76
GPR17	G protein-coupled receptor 17	0.8418	76
STK32A	Serine/threonine kinase 32A	0.8394	76
OLIG2	Oligodendrocyte transcription factor 2	0.8352	76
COL11A1	Collagen type XI alpha 1 chain	0.8245	76
UST	Uronyl 2-sulfotransferase	0.8147	76
TNR	Tenascin R	0.7917	76
KLHL1	Kelch like family member 1	0.7911	76
COL9A1	Collagen type IX alpha 1 chain	0.7868	76
OLIG1	Oligodendrocyte transcription factor 1	0.7839	76
BCAN	Brevican	0.7837	76
MEGF11	Multiple EGF like domains 11	0.7740	76
PLPP4	Phospholipid phosphatase 4	0.7715	76

IMMUNE CELLS

SEMA5A is part of cluster 8 Plasmacytoid DCs - Unknown function with confidenceⁱ 1
236 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.
SERPINF1	Serpin family F member 1	1.0000	8
GPR39	G protein-coupled receptor 39	1.0000	8
SLC35F3	Solute carrier family 35 member F3	1.0000	8
TLCD5	TLC domain containing 5	1.0000	8
TUBB6	Tubulin beta 6 class V	1.0000	8
SERINC2	Serine incorporator 2	1.0000	8
MAP1A	Microtubule associated protein 1A	1.0000	8
DNASE1L3	Deoxyribonuclease 1 like 3	1.0000	8
LARP1	La ribonucleoprotein 1, translational regulator	1.0000	8
NOPCHAP1	NOP protein chaperone 1	1.0000	8
GRAMD1B	GRAM domain containing 1B	1.0000	8
EIF2AK4	Eukaryotic translation initiation factor 2 alpha kinase 4	1.0000	8
LAMP5	Lysosomal associated membrane protein family member 5	1.0000	8
NDUFA8	NADH:ubiquinone oxidoreductase subunit A8	1.0000	8
RARRES2	Retinoic acid receptor responder 2	1.0000	8