Single cell type - CSF1 - 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.	CSF1
Gene descriptionⁱ Full gene name according to HGNC.	Colony stimulating factor 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Candidate cardiovascular disease genes Disease related genes Plasma proteins RAS pathway related 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. Read more	Intracellular,Membrane,Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	8

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. Read more	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. Read more	Cell type enhanced (granulocytes, Skeletal myocytes, Sertoli cells, Fibroblasts, Hepatic stellate cells)
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. Read more	Group enriched (eosinophil, basophil)
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in some
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Cell line enhanced (ASC diff, BJ hTERT+, GAMG, HHSteC, HSkMC, hTERT-RPE1)
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in many
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	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. Read more	Protein predicted to be secreted

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Cell type enhanced (granulocytes, Skeletal myocytes, Sertoli cells, Fibroblasts, Hepatic stellate cells)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

CSF1 is part of cluster 50 Fibroblasts - ECM organization with confidenceⁱ 1
441 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
MAP1LC3C	Microtubule associated protein 1 light chain 3 gamma	0.8176	50
ANGPTL2	Angiopoietin like 2	0.7812	50
IGFBP6	Insulin like growth factor binding protein 6	0.7656	50
ASPN	Asporin	0.7543	50
BOC	BOC cell adhesion associated, oncogene regulated	0.7526	50
ELN	Elastin	0.7470	50
COL6A3	Collagen type VI alpha 3 chain	0.7469	50
TNXB	Tenascin XB	0.7469	50
GSN	Gelsolin	0.7452	50
EN1	Engrailed homeobox 1	0.7451	50
PODN	Podocan	0.7429	50
GSC	Goosecoid homeobox	0.7428	50
PROCR	Protein C receptor	0.7416	50
MEDAG	Mesenteric estrogen dependent adipogenesis	0.7381	50
PI16	Peptidase inhibitor 16	0.7304	50

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	30.6 nTPM
Adipose tissue	38.4 nTPM
Breast	22.8 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	35.5 nTPM
Lung	35.5 nTPM

Astrocytes	11.8 nTPM
Brain	11.8 nTPM

B-cells	2.3 nTPM
Colon	6.4 nTPM
Breast	5.3 nTPM
Stomach	3.7 nTPM
Liver	2.5 nTPM
Adipose tissue	2.0 nTPM
Bone marrow	1.7 nTPM
Lymph node	1.5 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Spleen	0.0 nTPM

Dendritic cells	2.0 nTPM
Breast	4.7 nTPM
Adipose tissue	1.4 nTPM
PBMC	0.0 nTPM

Endothelial cells	21.6 nTPM
Skeletal muscle	37.2 nTPM
Lung	34.3 nTPM
Heart muscle	33.0 nTPM
Skin	32.9 nTPM
Liver	32.1 nTPM
Breast	28.4 nTPM
Esophagus	24.7 nTPM
Prostate	21.9 nTPM
Pancreas	15.5 nTPM
Endometrium	12.7 nTPM
Ovary	8.9 nTPM
Eye	8.1 nTPM
Testis	7.7 nTPM
Placenta	4.6 nTPM

Fibroblasts	58.9 nTPM
Adipose tissue	159.8 nTPM
Prostate	89.3 nTPM
Skeletal muscle	85.8 nTPM
Skin	77.7 nTPM
Stomach	75.7 nTPM
Esophagus	64.1 nTPM
Placenta	36.0 nTPM
Breast	25.7 nTPM
Heart muscle	17.1 nTPM
Lung	12.3 nTPM
Ovary	4.3 nTPM

Intestinal goblet cells	0.8 nTPM
Rectum	1.4 nTPM
Small intestine	1.1 nTPM
Colon	0.0 nTPM

Macrophages	8.2 nTPM
Lung	32.2 nTPM
Prostate	27.5 nTPM
Pancreas	25.5 nTPM
Endometrium	16.1 nTPM
Skeletal muscle	6.8 nTPM
Breast	6.0 nTPM
Ovary	3.2 nTPM
Spleen	2.1 nTPM
Esophagus	1.6 nTPM
Adipose tissue	1.3 nTPM
Kidney	0.8 nTPM
Testis	0.6 nTPM
PBMC	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	1.6 nTPM
Small intestine	3.7 nTPM
Rectum	1.0 nTPM
Colon	0.0 nTPM

Plasma cells	1.9 nTPM
Adipose tissue	7.0 nTPM
Spleen	1.3 nTPM
Stomach	1.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	1.1 nTPM
Bronchus	2.1 nTPM
Lung	0.0 nTPM

Smooth muscle cells	37.1 nTPM
Bronchus	88.1 nTPM
Adipose tissue	58.7 nTPM
Esophagus	55.8 nTPM
Prostate	43.5 nTPM
Skin	36.6 nTPM
Breast	31.0 nTPM
Skeletal muscle	26.7 nTPM
Endometrium	25.0 nTPM
Heart muscle	20.1 nTPM
Pancreas	14.6 nTPM
Ovary	7.8 nTPM

T-cells	20.9 nTPM
Prostate	52.1 nTPM
Stomach	49.1 nTPM
Esophagus	45.9 nTPM
Endometrium	30.3 nTPM
Bone marrow	23.6 nTPM
Spleen	23.2 nTPM
Skin	23.0 nTPM
Colon	22.8 nTPM
Skeletal muscle	18.5 nTPM
Breast	18.3 nTPM
Lung	18.2 nTPM
Adipose tissue	9.0 nTPM
Lymph node	7.3 nTPM
Liver	5.4 nTPM
Kidney	4.7 nTPM
Ovary	2.2 nTPM
PBMC	1.5 nTPM

Basal keratinocytes	7.4 nTPM
Skin	7.4 nTPM

Basal prostatic cells	5.1 nTPM
Prostate	5.1 nTPM

Basal respiratory cells	7.9 nTPM
Bronchus	7.9 nTPM

Basal squamous epithelial cells	13.1 nTPM
Esophagus	13.1 nTPM

Undifferentiated cells	1.0 nTPM
Colon	1.3 nTPM
Small intestine	1.3 nTPM
Rectum	0.5 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC