Single cell type - CHD6 - 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.	CHD6
Gene descriptionⁱ Full gene name according to HGNC.	Chromodomain helicase DNA binding protein 6
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Plasma proteins Potential drug targets
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.	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. Read more	Non-specific - Transcription (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	Low cell type specificity
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 many
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: Low cell type specificity

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

CHD6 is part of cluster 52 Non-specific - Transcription with confidenceⁱ 1
611 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
KCNAB3	Potassium voltage-gated channel subfamily A regulatory beta subunit 3	0.5361	62
KIAA2026	KIAA2026	0.4930	52
GDF11	Growth differentiation factor 11	0.4908	56
BPTF	Bromodomain PHD finger transcription factor	0.4823	52
CREBZF	CREB/ATF bZIP transcription factor	0.4815	52
HRNR	Hornerin	0.4790	46
NAA16	N-alpha-acetyltransferase 16, NatA auxiliary subunit	0.4761	52
BOD1L1	Biorientation of chromosomes in cell division 1 like 1	0.4727	52
HCN2	Hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2	0.4723	56
LUC7L3	LUC7 like 3 pre-mRNA splicing factor	0.4702	52
NKTR	Natural killer cell triggering receptor	0.4701	52
CWF19L2	CWF19 like cell cycle control factor 2	0.4687	52
FAM184B	Family with sequence similarity 184 member B	0.4686	68
KMT2A	Lysine methyltransferase 2A	0.4562	52
PNISR	PNN interacting serine and arginine rich protein	0.4495	52

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	42.2 nTPM
Adipose tissue	45.6 nTPM
Breast	39.0 nTPM

Alveolar cells type 1	48.1 nTPM
Lung	48.1 nTPM

Alveolar cells type 2	30.8 nTPM
Lung	30.8 nTPM

Astrocytes	148.2 nTPM
Brain	148.2 nTPM

B-cells	42.8 nTPM
Adipose tissue	85.2 nTPM
Colon	59.1 nTPM
Bone marrow	44.9 nTPM
Breast	42.8 nTPM
PBMC	41.4 nTPM
Lymph node	39.5 nTPM
Stomach	37.7 nTPM
Spleen	31.8 nTPM
Kidney	23.8 nTPM
Liver	21.7 nTPM

Dendritic cells	53.3 nTPM
Adipose tissue	76.0 nTPM
Breast	48.1 nTPM
PBMC	35.8 nTPM

Endothelial cells	36.5 nTPM
Heart muscle	61.3 nTPM
Skeletal muscle	55.8 nTPM
Testis	51.6 nTPM
Endometrium	44.1 nTPM
Lung	40.6 nTPM
Ovary	36.6 nTPM
Liver	35.7 nTPM
Breast	35.7 nTPM
Eye	34.8 nTPM
Placenta	28.4 nTPM
Prostate	26.8 nTPM
Esophagus	24.7 nTPM
Skin	22.9 nTPM
Pancreas	11.6 nTPM

Fibroblasts	33.8 nTPM
Heart muscle	51.3 nTPM
Skeletal muscle	42.5 nTPM
Adipose tissue	41.2 nTPM
Breast	41.0 nTPM
Lung	35.7 nTPM
Skin	32.2 nTPM
Placenta	29.4 nTPM
Esophagus	29.0 nTPM
Prostate	28.0 nTPM
Ovary	27.0 nTPM
Stomach	14.9 nTPM

Intestinal goblet cells	35.9 nTPM
Colon	43.6 nTPM
Rectum	37.2 nTPM
Small intestine	27.0 nTPM

Macrophages	27.5 nTPM
Adipose tissue	50.9 nTPM
Skeletal muscle	43.5 nTPM
Endometrium	37.9 nTPM
Ovary	34.6 nTPM
Breast	33.3 nTPM
Testis	29.7 nTPM
Lung	29.0 nTPM
Esophagus	26.8 nTPM
Spleen	26.0 nTPM
Bone marrow	25.0 nTPM
Kidney	21.9 nTPM
Pancreas	20.4 nTPM
Stomach	17.6 nTPM
Prostate	16.0 nTPM
PBMC	0.0 nTPM

Paneth cells	16.0 nTPM
Rectum	19.9 nTPM
Small intestine	15.0 nTPM
Colon	13.2 nTPM

Plasma cells	32.3 nTPM
Adipose tissue	85.8 nTPM
Stomach	28.5 nTPM
Esophagus	24.6 nTPM
Spleen	14.7 nTPM
Bone marrow	8.2 nTPM

Respiratory ciliated cells	35.6 nTPM
Lung	49.5 nTPM
Bronchus	21.8 nTPM

Smooth muscle cells	44.4 nTPM
Heart muscle	73.5 nTPM
Adipose tissue	57.9 nTPM
Endometrium	56.8 nTPM
Skeletal muscle	55.2 nTPM
Ovary	46.3 nTPM
Bronchus	42.3 nTPM
Esophagus	41.9 nTPM
Breast	40.6 nTPM
Skin	32.1 nTPM
Prostate	29.1 nTPM
Pancreas	13.2 nTPM

T-cells	45.5 nTPM
Adipose tissue	83.9 nTPM
Endometrium	69.4 nTPM
Skeletal muscle	67.7 nTPM
PBMC	57.9 nTPM
Colon	57.5 nTPM
Breast	49.3 nTPM
Lung	47.1 nTPM
Ovary	42.2 nTPM
Esophagus	39.3 nTPM
Skin	38.7 nTPM
Lymph node	37.5 nTPM
Liver	36.9 nTPM
Stomach	35.3 nTPM
Kidney	34.2 nTPM
Spleen	29.0 nTPM
Bone marrow	28.9 nTPM
Prostate	19.0 nTPM

Basal keratinocytes	18.1 nTPM
Skin	18.1 nTPM

Basal prostatic cells	38.6 nTPM
Prostate	38.6 nTPM

Basal respiratory cells	30.3 nTPM
Bronchus	30.3 nTPM

Basal squamous epithelial cells	37.0 nTPM
Esophagus	37.0 nTPM

Undifferentiated cells	24.5 nTPM
Colon	28.6 nTPM
Small intestine	22.7 nTPM
Rectum	22.0 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