Single cell type - OLFML1 - 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.	OLFML1
Gene descriptionⁱ Full gene name according to HGNC.	Olfactomedin like 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.	Secreted
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.	Fibroblasts - ECM organization (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 (Fibroblasts, Leydig cells, Peritubular cells, Ovarian stromal cells, Smooth muscle cells, Lymphatic endothelial cells, Endometrial stromal cells, Mesothelial 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.	0.84
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.	Group enriched (Pericyte, Fibroblast, Vascular associated smooth muscle cell, Choroid plexus epithelial cell)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

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: Group enriched (Fibroblasts, Leydig cells, Peritubular cells, Ovarian stromal cells, Smooth muscle cells, Lymphatic endothelial cells, Endometrial stromal cells, Mesothelial 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: Group enriched (Pericyte, Fibroblast, Vascular associated smooth muscle cell, Choroid plexus epithelial cell)

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

OLFML1 is part of cluster 53 Fibroblasts - ECM organization with confidenceⁱ 1
305 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.
PLAC9	Placenta associated 9	0.9009	53
DCN	Decorin	0.8834	53
CFD	Complement factor D	0.8527	53
HTRA3	HtrA serine peptidase 3	0.8471	53
MAP1LC3C	Microtubule associated protein 1 light chain 3 gamma	0.8352	53
MYOC	Myocilin	0.8308	53
PDGFRL	Platelet derived growth factor receptor like	0.8285	53
VEGFD	Vascular endothelial growth factor D	0.8270	53
GSC	Goosecoid homeobox	0.8226	53
TNXB	Tenascin XB	0.8122	53
COL6A3	Collagen type VI alpha 3 chain	0.8107	53
ANGPTL2	Angiopoietin like 2	0.8099	53
GSN	Gelsolin	0.8060	53
LRRN4CL	LRRN4 C-terminal like	0.8027	53
COL6A6	Collagen type VI alpha 6 chain	0.8025	53

IMMUNE CELLS

OLFML1 is part of cluster 23 B-cells - Immunoglobulins with confidenceⁱ 0.95
208 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.
MEF2C	Myocyte enhancer factor 2C	1.0000	23
RUBCNL	Rubicon like autophagy enhancer	1.0000	23
UVRAG	UV radiation resistance associated	0.9762	23
DOP1B	DOP1 leucine zipper like protein B	0.9762	23
NCOA3	Nuclear receptor coactivator 3	0.9762	23
PIERCE2	Piercer of microtubule wall 2	0.9524	23
ARHGAP24	Rho GTPase activating protein 24	0.9524	23
BTN2A2	Butyrophilin subfamily 2 member A2	0.9524	23
MOB3B	MOB kinase activator 3B	0.9524	23
TRIM38	Tripartite motif containing 38	0.9524	23
EPB41L2	Erythrocyte membrane protein band 4.1 like 2	0.9524	23
CD40	CD40 molecule	0.9286	23
DYRK4	Dual specificity tyrosine phosphorylation regulated kinase 4	0.9286	23
GNA12	G protein subunit alpha 12	0.9286	23
USP6NL	USP6 N-terminal like	0.9286	23