Single cell type - SPECC1L - 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.	SPECC1L
Gene descriptionⁱ Full gene name according to HGNC.	Sperm antigen with calponin homology and coiled-coil domains 1 like
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes 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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	6

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.	Non-specific - Basic cellular functions (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.	Group enriched (Bergmann glia, Choroid plexus epithelial cells, Microglia, Brain excitatory neurons, Oligodendrocyte progenitor cells, Astrocytes, Brain inhibitory neurons, Oligodendrocytes, Ependymal cells, Other brain 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.	0.77
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.	Low cell type specificity
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.	Low immune cell specificity
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 (nCPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. * Single nuclei Read more
Single cell type groups RNA single cell type group specificity: Group enriched (Glial cells, Ciliated cells, Neuronal 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: Low cell type specificity

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: Low immune cell specificity
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

SPECC1L is part of cluster 22 Non-specific - Basic cellular functions with confidenceⁱ 1
156 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.
ANKHD1	Ankyrin repeat and KH domain containing 1	0.8620	22
ZC3H11A	Zinc finger CCCH-type containing 11A	0.8416	22
VPS33A	VPS33A core subunit of CORVET and HOPS complexes	0.8262	22
ZNF410	Zinc finger protein 410	0.8240	22
RBM14	RNA binding motif protein 14	0.8097	22
ISY1	ISY1 splicing factor homolog	0.7619	22
RNF31	Ring finger protein 31	0.7586	22
TMEM265	Transmembrane protein 265	0.7580	22
AP3S2	Adaptor related protein complex 3 subunit sigma 2	0.7531	22
RBAK	RB associated KRAB zinc finger	0.7510	22
DEPDC5	DEP domain containing 5, GATOR1 subcomplex subunit	0.7509	22
MED17	Mediator complex subunit 17	0.7469	22
SLC33A1	Solute carrier family 33 member 1	0.7440	22
TSNAX	Translin associated factor X	0.7402	22
ST3GAL3	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	0.7117	22

IMMUNE CELLS

SPECC1L is part of cluster 42 Non-specific - Vesicular transport with confidenceⁱ 1
519 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.
METTL14	Methyltransferase 14, N6-adenosine-methyltransferase subunit	1.0000	42
FBXO28	F-box protein 28	1.0000	42
SMC4	Structural maintenance of chromosomes 4	1.0000	42
ZC3H7A	Zinc finger CCCH-type containing 7A	1.0000	42
TES	Testin LIM domain protein	1.0000	42
RNF168	Ring finger protein 168	0.9762	42
AP5M1	Adaptor related protein complex 5 subunit mu 1	0.9762	42
TOPBP1	DNA topoisomerase II binding protein 1	0.9762	42
CCDC82	Coiled-coil domain containing 82	0.9762	42
MINDY3	MINDY lysine 48 deubiquitinase 3	0.9762	42
RNASEL	Ribonuclease L	0.9762	42
IMPA1	Inositol monophosphatase 1	0.9762	42
BLZF1	Basic leucine zipper nuclear factor 1	0.9762	42
SMAP1	Small ArfGAP 1	0.9762	42
PARP4	Poly(ADP-ribose) polymerase family member 4	0.9762	42