Single cell type - CHI3L1 - 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.	CHI3L1
Gene descriptionⁱ Full gene name according to HGNC.	Chitinase 3 like 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Disease related genes Human disease related genes Metabolic proteins 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. Read more	Intracellular,Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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	Macrophages - Innate immune response (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 (Hofbauer cells, Ductal cells, Basal respiratory cells, Hepatocytes)
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	Immune cell enriched (neutrophil)
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 single
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, ASC TERT1, HSkMC, THP-1, U-138 MG, U-87 MG)
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 some
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 (Hofbauer cells, Ductal cells, Basal respiratory cells, Hepatocytes)

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

CHI3L1 is part of cluster 4 Macrophages - Innate immune response with confidenceⁱ 1
228 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
SERPINA3	Serpin family A member 3	0.7337	50
P2RX2	Purinergic receptor P2X 2	0.6919	50
CCL11	C-C motif chemokine ligand 11	0.6761	50
C1QTNF5	C1q and TNF related 5	0.6731	50
CPZ	Carboxypeptidase Z	0.6614	50
ANGPTL7	Angiopoietin like 7	0.6590	50
DNASE2	Deoxyribonuclease 2, lysosomal	0.6182	4
APOD	Apolipoprotein D	0.6122	50
PSAP	Prosaposin	0.6030	4
SFRP2	Secreted frizzled related protein 2	0.5986	50
SERPING1	Serpin family G member 1	0.5957	2
KERA	Keratocan	0.5918	50
CXCL5	C-X-C motif chemokine ligand 5	0.5854	4
SLC43A3	Solute carrier family 43 member 3	0.5846	4
DCANP1	Dendritic cell associated nuclear protein	0.5843	4

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	0.7 nTPM
Breast	1.1 nTPM
Adipose tissue	0.3 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	42.8 nTPM
Lung	42.8 nTPM

Astrocytes	20.5 nTPM
Brain	20.5 nTPM

B-cells	0.1 nTPM
Liver	1.3 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Breast	0.0 nTPM

Dendritic cells	0.6 nTPM
Breast	1.8 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM

Endothelial cells	2.1 nTPM
Placenta	15.9 nTPM
Breast	8.0 nTPM
Eye	1.6 nTPM
Prostate	1.1 nTPM
Heart muscle	0.9 nTPM
Liver	0.9 nTPM
Endometrium	0.7 nTPM
Skin	0.4 nTPM
Skeletal muscle	0.2 nTPM
Lung	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Fibroblasts	18.6 nTPM
Esophagus	82.7 nTPM
Prostate	28.5 nTPM
Skeletal muscle	25.2 nTPM
Adipose tissue	20.3 nTPM
Breast	19.7 nTPM
Lung	19.0 nTPM
Placenta	7.6 nTPM
Heart muscle	2.0 nTPM
Skin	0.1 nTPM
Ovary	0.0 nTPM
Stomach	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Macrophages	23.7 nTPM
Pancreas	201.6 nTPM
Breast	115.2 nTPM
Kidney	12.9 nTPM
Lung	8.2 nTPM
Endometrium	4.8 nTPM
Bone marrow	3.7 nTPM
Prostate	3.4 nTPM
Adipose tissue	2.7 nTPM
Skeletal muscle	1.5 nTPM
Ovary	1.2 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Esophagus	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	1.4 nTPM
Esophagus	6.1 nTPM
Adipose tissue	0.6 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	3.4 nTPM
Lung	4.4 nTPM
Bronchus	2.5 nTPM

Smooth muscle cells	2.3 nTPM
Bronchus	8.4 nTPM
Pancreas	5.2 nTPM
Adipose tissue	4.5 nTPM
Heart muscle	2.6 nTPM
Prostate	1.9 nTPM
Breast	1.4 nTPM
Endometrium	1.1 nTPM
Skeletal muscle	0.5 nTPM
Ovary	0.1 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM

T-cells	0.9 nTPM
Lung	9.1 nTPM
Kidney	2.7 nTPM
Breast	2.1 nTPM
Skeletal muscle	1.0 nTPM
Endometrium	0.5 nTPM
Liver	0.2 nTPM
Bone marrow	0.1 nTPM
Colon	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Cholangiocytes	2.8 nTPM
Liver	2.8 nTPM

Collecting duct cells	27.6 nTPM
Kidney	27.6 nTPM

Endometrial stromal cells	2.2 nTPM
Endometrium	2.2 nTPM

Undifferentiated cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 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