Single cell type - CLIP2 - 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.	CLIP2
Gene descriptionⁱ Full gene name according to HGNC.	CAP-Gly domain containing linker protein 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes Plasma proteins
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.	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.	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 enhanced (Oligodendrocytes, Oligodendrocyte precursor cells, Excitatory neurons, Inhibitory 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.	0.63
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.	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 (Oligodendrocytes, Oligodendrocyte precursor cells, Excitatory neurons, Inhibitory neurons)

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: 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

CLIP2 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.
MYO5A	Myosin VA	0.5402	34
MOB3B	MOB kinase activator 3B	0.5305	51
DEFB109B	Defensin beta 109B	0.5166	51
SYNDIG1	Synapse differentiation inducing 1	0.4973	51
PTP4A1	Protein tyrosine phosphatase 4A1	0.4960	51
BNIP5	BCL2 interacting protein 5	0.4930	5
UBE2E2	Ubiquitin conjugating enzyme E2 E2	0.4923	51
PEAK1	Pseudopodium enriched atypical kinase 1	0.4914	76
TICAM1	TIR domain containing adaptor molecule 1	0.4866	5
ARL14	ADP ribosylation factor like GTPase 14	0.4843	5
BCAS1	Brain enriched myelin associated protein 1	0.4789	16
ZDHHC14	Zinc finger DHHC-type palmitoyltransferase 14	0.4773	76
OR6C70	Olfactory receptor family 6 subfamily C member 70	0.4715	34
GTDC1	Glycosyltransferase like domain containing 1	0.4714	34
ZSWIM6	Zinc finger SWIM-type containing 6	0.4668	76

IMMUNE CELLS

CLIP2 is part of cluster 40 Monocytes - Innate immune response with confidenceⁱ 0.89
228 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.
PAQR4	Progestin and adipoQ receptor family member 4	0.9762	40
WASF2	WASP family member 2	0.9762	40
POU2F2	POU class 2 homeobox 2	0.9762	40
EGR2	Early growth response 2	0.9524	40
TICAM2	TIR domain containing adaptor molecule 2	0.9524	40
CALHM6	Calcium homeostasis modulator family member 6	0.9524	40
AFMID	Arylformamidase	0.9524	40
RAB39A	RAB39A, member RAS oncogene family	0.9524	40
MTSS1	MTSS I-BAR domain containing 1	0.9524	40
SCIMP	SLP adaptor and CSK interacting membrane protein	0.9524	40
JDP2	Jun dimerization protein 2	0.9524	40
RASL11A	RAS like family 11 member A	0.9524	40
GORASP1	Golgi reassembly stacking protein 1	0.9524	40
HBEGF	Heparin binding EGF like growth factor	0.9524	40
SYNGR2	Synaptogyrin 2	0.9524	40