Single cell type - CHID1 - 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.	CHID1
Gene descriptionⁱ Full gene name according to HGNC.	Chitinase domain containing 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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	14

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	Spermatocytes & Spermatogonia - Spermatogenesis (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 (Late spermatids)
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	Low immune cell specificity
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 all
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	Low cell line specificity
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 all
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

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 (Late spermatids)

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

CHID1 is part of cluster 13 Spermatocytes & Spermatogonia - Spermatogenesis with confidenceⁱ 1
231 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
DPP7	Dipeptidyl peptidase 7	0.6201	25
INCA1	Inhibitor of CDK, cyclin A1 interacting protein 1	0.5926	13
PRDX4	Peroxiredoxin 4	0.5876	55
PIGP	Phosphatidylinositol glycan anchor biosynthesis class P	0.5674	13
SPCS1	Signal peptidase complex subunit 1	0.5432	25
PEX10	Peroxisomal biogenesis factor 10	0.5388	25
MEIOC	Meiosis specific with coiled-coil domain	0.5290	13
BET1L	Bet1 golgi vesicular membrane trafficking protein like	0.5251	31
PRSS21	Serine protease 21	0.5216	13
TMEM147	Transmembrane protein 147	0.5169	10
MEIOB	Meiosis specific with OB-fold	0.5131	13
GINM1	Glycoprotein integral membrane 1	0.5130	25
CREB3	CAMP responsive element binding protein 3	0.5007	25
SYCP1	Synaptonemal complex protein 1	0.4975	13
C5orf47	Chromosome 5 open reading frame 47	0.4958	13

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	33.0 nTPM
Breast	43.6 nTPM
Adipose tissue	22.4 nTPM

Alveolar cells type 1	41.7 nTPM
Lung	41.7 nTPM

Alveolar cells type 2	36.7 nTPM
Lung	36.7 nTPM

Astrocytes	4.2 nTPM
Brain	4.2 nTPM

B-cells	28.6 nTPM
Liver	90.7 nTPM
Breast	74.9 nTPM
Kidney	28.5 nTPM
Colon	20.8 nTPM
Stomach	20.0 nTPM
Spleen	14.9 nTPM
Bone marrow	14.7 nTPM
PBMC	8.5 nTPM
Lymph node	7.1 nTPM
Adipose tissue	6.0 nTPM

Dendritic cells	34.4 nTPM
PBMC	63.8 nTPM
Breast	24.1 nTPM
Adipose tissue	15.4 nTPM

Endothelial cells	31.5 nTPM
Placenta	55.7 nTPM
Pancreas	50.2 nTPM
Breast	44.2 nTPM
Liver	37.6 nTPM
Ovary	34.6 nTPM
Eye	34.0 nTPM
Testis	32.3 nTPM
Endometrium	30.8 nTPM
Skin	27.5 nTPM
Prostate	26.2 nTPM
Lung	18.7 nTPM
Skeletal muscle	18.7 nTPM
Esophagus	16.5 nTPM
Heart muscle	13.8 nTPM

Fibroblasts	69.6 nTPM
Placenta	121.6 nTPM
Breast	109.1 nTPM
Ovary	87.2 nTPM
Skin	74.6 nTPM
Stomach	69.8 nTPM
Adipose tissue	69.1 nTPM
Esophagus	67.6 nTPM
Skeletal muscle	53.9 nTPM
Prostate	50.5 nTPM
Lung	34.7 nTPM
Heart muscle	27.7 nTPM

Intestinal goblet cells	42.8 nTPM
Rectum	45.6 nTPM
Small intestine	42.1 nTPM
Colon	40.7 nTPM

Macrophages	34.0 nTPM
Ovary	122.7 nTPM
Pancreas	46.0 nTPM
Kidney	40.9 nTPM
Breast	36.2 nTPM
Prostate	34.4 nTPM
Adipose tissue	33.7 nTPM
Esophagus	31.5 nTPM
Testis	29.1 nTPM
Skeletal muscle	26.5 nTPM
Endometrium	22.5 nTPM
Bone marrow	22.5 nTPM
Lung	22.3 nTPM
Spleen	20.7 nTPM
Stomach	20.5 nTPM
PBMC	0.0 nTPM

Paneth cells	43.2 nTPM
Rectum	61.2 nTPM
Small intestine	48.8 nTPM
Colon	19.7 nTPM

Plasma cells	123.7 nTPM
Stomach	220.6 nTPM
Esophagus	190.9 nTPM
Spleen	108.6 nTPM
Bone marrow	57.7 nTPM
Adipose tissue	40.7 nTPM

Respiratory ciliated cells	45.7 nTPM
Bronchus	57.9 nTPM
Lung	33.5 nTPM

Smooth muscle cells	41.7 nTPM
Ovary	82.4 nTPM
Pancreas	72.5 nTPM
Bronchus	47.7 nTPM
Breast	44.2 nTPM
Adipose tissue	37.6 nTPM
Prostate	34.0 nTPM
Skin	30.0 nTPM
Heart muscle	29.9 nTPM
Esophagus	27.9 nTPM
Endometrium	27.6 nTPM
Skeletal muscle	24.4 nTPM

T-cells	19.2 nTPM
Kidney	41.1 nTPM
Ovary	37.8 nTPM
Liver	25.6 nTPM
Colon	24.7 nTPM
Breast	21.6 nTPM
Stomach	21.4 nTPM
PBMC	20.8 nTPM
Spleen	18.2 nTPM
Endometrium	18.1 nTPM
Skin	18.0 nTPM
Bone marrow	18.0 nTPM
Lung	15.2 nTPM
Skeletal muscle	12.7 nTPM
Adipose tissue	12.7 nTPM
Lymph node	11.5 nTPM
Prostate	9.5 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	22.8 nTPM
Skin	22.8 nTPM

Basal prostatic cells	62.2 nTPM
Prostate	62.2 nTPM

Basal respiratory cells	78.9 nTPM
Bronchus	78.9 nTPM

Basal squamous epithelial cells	22.2 nTPM
Esophagus	22.2 nTPM

Undifferentiated cells	59.9 nTPM
Small intestine	69.4 nTPM
Rectum	66.5 nTPM
Colon	43.8 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