Single cell type - CPSF2 - 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.	CPSF2
Gene descriptionⁱ Full gene name according to HGNC.	Cleavage and polyadenylation specific factor 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	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.	Non-specific - Basic cellular processes (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.	Low cell type specificity
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.	0.27
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 (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: Low cell type specificity

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

CPSF2 is part of cluster 39 Non-specific - Basic cellular processes with confidenceⁱ 1
835 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.
MED1	Mediator complex subunit 1	0.5195	39
MTDH	Metadherin	0.4970	77
DNAJC13	DnaJ heat shock protein family (Hsp40) member C13	0.4822	58
DDX42	DEAD-box helicase 42	0.4723	39
GAPVD1	GTPase activating protein and VPS9 domains 1	0.4720	55
TAOK1	TAO kinase 1	0.4714	55
SYNCRIP	Synaptotagmin binding cytoplasmic RNA interacting protein	0.4653	39
VMA21	Vacuolar ATPase assembly factor VMA21	0.4613	29
KPNB1	Karyopherin subunit beta 1	0.4593	39
CCAR1	Cell division cycle and apoptosis regulator 1	0.4586	39
LILRA6	Leukocyte immunoglobulin like receptor A6	0.4558	29
BLTP2	Bridge-like lipid transfer protein family member 2	0.4549	33
CGGBP1	CGG triplet repeat binding protein 1	0.4539	55
AGO1	Argonaute RISC component 1	0.4532	29
API5	Apoptosis inhibitor 5	0.4524	49

IMMUNE CELLS

CPSF2 is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 0.51
501 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.
H2AJ	H2A.J histone	0.9762	10
AHNAK	AHNAK nucleoprotein	0.9762	38
BCKDHA	Branched chain keto acid dehydrogenase E1 subunit alpha	0.9524	38
CDC37	Cell division cycle 37, HSP90 cochaperone	0.9524	10
SLC26A6	Solute carrier family 26 member 6	0.9524	10
NARS1	Asparaginyl-tRNA synthetase 1	0.9524	38
FHOD1	Formin homology 2 domain containing 1	0.9524	10
MGAT1	Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase	0.9286	38
ARPC4	Actin related protein 2/3 complex subunit 4	0.9286	38
TPP1	Tripeptidyl peptidase 1	0.9286	10
FAM151B	Family with sequence similarity 151 member B	0.9286	38
MAN2C1	Mannosidase alpha class 2C member 1	0.9286	33
LAP3	Leucine aminopeptidase 3	0.9286	10
ACSS2	Acyl-CoA synthetase short chain family member 2	0.9286	26
CD68	CD68 molecule	0.9286	38