Single cell type - ABLIM1 - 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.	ABLIM1
Gene descriptionⁱ Full gene name according to HGNC.	Actin binding LIM protein 1
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.	11

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.	Astrocytes - 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 (Astrocytes, Cardiomyocytes, Squamous epithelial cells, Peritubular 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.	0.44
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 (Astrocyte)
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 enhanced (naive CD4 T-cell)
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 (Astrocytes, Cardiomyocytes, Squamous epithelial cells, Peritubular 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 (Astrocyte)

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 enhanced (naive CD4 T-cell)
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

ABLIM1 is part of cluster 47 Astrocytes - Unknown function with confidenceⁱ 1
196 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.
PRICKLE4	Prickle planar cell polarity protein 4	0.5373	47
PIRT	Phosphoinositide interacting regulator of transient receptor potential channels	0.5185	47
PHKA1	Phosphorylase kinase regulatory subunit alpha 1	0.5010	47
RAPGEF3	Rap guanine nucleotide exchange factor 3	0.4956	41
CACHD1	Cache domain containing 1	0.4928	47
ZDHHC15	Zinc finger DHHC-type palmitoyltransferase 15	0.4769	68
ASAP3	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	0.4722	4
TOM1L2	Target of myb1 like 2 membrane trafficking protein	0.4527	47
NEBL	Nebulette	0.4488	68
RPL36A-HNRNPH2	RPL36A-HNRNPH2 readthrough	0.4384	47
RGMA	Repulsive guidance molecule BMP co-receptor a	0.4355	53
ARHGEF4	Rho guanine nucleotide exchange factor 4	0.4352	47
GLI2	GLI family zinc finger 2	0.4343	6
SMARCA2	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	0.4282	55
CAMK2D	Calcium/calmodulin dependent protein kinase II delta	0.4259	68

IMMUNE CELLS

ABLIM1 is part of cluster 43 Non-specific - Transcription & Translation with confidenceⁱ 0.92
433 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.
MCMDC2	Minichromosome maintenance domain containing 2	1.0000	43
TRMT11	TRNA methyltransferase 11 homolog	1.0000	43
RNF212	Ring finger protein 212	1.0000	43
RPL9	Ribosomal protein L9	1.0000	43
USP53	Ubiquitin specific peptidase 53	1.0000	43
CRTC3	CREB regulated transcription coactivator 3	1.0000	43
BEX2	Brain expressed X-linked 2	1.0000	43
RPL3	Ribosomal protein L3	0.9762	43
BCL9	BCL9 transcription coactivator	0.9762	43
LZTS2	Leucine zipper tumor suppressor 2	0.9762	24
SLC39A14	Solute carrier family 39 member 14	0.9762	43
TSPAN6	Tetraspanin 6	0.9762	43
CBY1	Chibby family member 1, beta catenin antagonist	0.9762	24
SEC14L2	SEC14 like lipid binding 2	0.9762	24
C3orf18	Chromosome 3 open reading frame 18	0.9762	43