Single cell type - KDM5D - 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.	KDM5D
Gene descriptionⁱ Full gene name according to HGNC.	Lysine demethylase 5D
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Plasma proteins Transcription factors
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.	6

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	NK-cells & T-cells - 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 (Plasma 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	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	Cell line enhanced (HEL, U-698)
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

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 (Plasma 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

KDM5D is part of cluster 63 NK-cells & T-cells - Immune response with confidenceⁱ 1
362 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
UTY	Ubiquitously transcribed tetratricopeptide repeat containing, Y-linked	0.6617	59
ZFY	Zinc finger protein Y-linked	0.5620	59
POLR2J3	RNA polymerase II subunit J3	0.5301	52
PRR4	Proline rich 4	0.5289	9
RPS4Y1	Ribosomal protein S4 Y-linked 1	0.5056	32
ATXN7	Ataxin 7	0.4947	63
USP9Y	Ubiquitin specific peptidase 9 Y-linked	0.4850	21
DDX19A	DEAD-box helicase 19A	0.4803	52
CD27	CD27 molecule	0.4551	55
ARL5A	ADP ribosylation factor like GTPase 5A	0.4481	55
RINL	Ras and Rab interactor like	0.4402	63
CRTC3	CREB regulated transcription coactivator 3	0.4340	63
CYB561D1	Cytochrome b561 family member D1	0.4329	63
LIN37	Lin-37 DREAM MuvB core complex component	0.4315	59
PIM2	Pim-2 proto-oncogene, serine/threonine kinase	0.4301	55

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	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	16.5 nTPM
Lung	16.5 nTPM

Astrocytes	9.4 nTPM
Brain	9.4 nTPM

B-cells	22.2 nTPM
PBMC	37.1 nTPM
Bone marrow	33.5 nTPM
Stomach	32.7 nTPM
Liver	30.1 nTPM
Kidney	28.5 nTPM
Spleen	26.0 nTPM
Lymph node	21.3 nTPM
Colon	12.8 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Dendritic cells	14.6 nTPM
PBMC	43.8 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Endothelial cells	10.8 nTPM
Testis	18.7 nTPM
Heart muscle	17.5 nTPM
Liver	16.5 nTPM
Prostate	15.8 nTPM
Lung	15.6 nTPM
Esophagus	13.9 nTPM
Skin	13.5 nTPM
Pancreas	11.6 nTPM
Eye	11.3 nTPM
Skeletal muscle	10.6 nTPM
Placenta	4.6 nTPM
Ovary	1.1 nTPM
Endometrium	0.0 nTPM
Breast	0.0 nTPM

Fibroblasts	10.6 nTPM
Esophagus	19.8 nTPM
Lung	17.9 nTPM
Stomach	17.8 nTPM
Prostate	15.8 nTPM
Skin	14.8 nTPM
Heart muscle	12.0 nTPM
Skeletal muscle	11.8 nTPM
Placenta	6.3 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Intestinal goblet cells	5.8 nTPM
Small intestine	11.5 nTPM
Colon	5.8 nTPM
Rectum	0.0 nTPM

Macrophages	10.3 nTPM
Esophagus	26.8 nTPM
Stomach	26.4 nTPM
Bone marrow	17.5 nTPM
Testis	17.4 nTPM
Lung	15.0 nTPM
Spleen	14.5 nTPM
Kidney	14.3 nTPM
Prostate	12.6 nTPM
Skeletal muscle	7.3 nTPM
Pancreas	2.5 nTPM
PBMC	0.0 nTPM
Endometrium	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Paneth cells	5.0 nTPM
Small intestine	15.0 nTPM
Colon	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	46.3 nTPM
Bone marrow	67.6 nTPM
Stomach	63.6 nTPM
Spleen	50.7 nTPM
Esophagus	49.4 nTPM
Adipose tissue	0.0 nTPM

Respiratory ciliated cells	5.5 nTPM
Bronchus	6.6 nTPM
Lung	4.4 nTPM

Smooth muscle cells	8.5 nTPM
Prostate	25.4 nTPM
Skin	19.9 nTPM
Esophagus	18.6 nTPM
Skeletal muscle	15.7 nTPM
Heart muscle	8.6 nTPM
Bronchus	4.8 nTPM
Pancreas	1.0 nTPM
Endometrium	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

T-cells	16.4 nTPM
PBMC	36.2 nTPM
Bone marrow	32.5 nTPM
Prostate	23.6 nTPM
Lung	22.8 nTPM
Stomach	22.6 nTPM
Spleen	22.4 nTPM
Liver	20.8 nTPM
Lymph node	20.1 nTPM
Esophagus	19.7 nTPM
Kidney	16.4 nTPM
Colon	16.1 nTPM
Skin	15.2 nTPM
Skeletal muscle	10.7 nTPM
Endometrium	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Basal keratinocytes	6.4 nTPM
Skin	6.4 nTPM

Basal prostatic cells	9.2 nTPM
Prostate	9.2 nTPM

Basal respiratory cells	5.3 nTPM
Bronchus	5.3 nTPM

Basal squamous epithelial cells	18.2 nTPM
Esophagus	18.2 nTPM

Undifferentiated cells	6.6 nTPM
Small intestine	16.1 nTPM
Colon	3.8 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